Dear all,
I am analyzing chipseq data and I am trying to use bayespeak package
for
peak detection.
The code that I am using is
#call libraries
library(GenomicRanges)
Library(BayesPeak)
library(ShortRead)
library(chipseq)
library(ChIPpeakAnno)
library(multicore)
library(GenomicFeatures)
#read sample JKA
JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique
_forfastq.fastq_SAM",
overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_fil
tered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA<-readBamGappedAlignments(JKA)
IRanges_JKA<-ranges(Granges_JKA)
#read Input JKA
JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM",
overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_fil
tered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA_I<-readBamGappedAlignments(JKA_I)
IRanges_JKA_I<-ranges(Granges_JKA_I)
#Peak Calling with BayesPeak
raw.output <- bayespeak(treatment=JKA, control=JKA_I,use.multicore =
TRUE,
mc.cores = 4)
after the last command I am getting the forllowing error:
Error in substring(temp[1], 1, 5) : invalid multibyte string at '<ed>'
I also tried to remove the use of parallelization but the error
remains the
same, can someone tell me what I am doing wrong ?
thanks for the help,
Andreia
bellow is the information concerning sessionInfo
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BayesPeak_1.4.0 GenomicFeatures_1.4.3
[3] multicore_0.1-5 ChIPpeakAnno_1.8.0
[5] limma_3.8.2 org.Hs.eg.db_2.5.0
[7] GO.db_2.4.1 RSQLite_0.9-1
[9] DBI_0.2-5 AnnotationDbi_1.14.1
[11] BSgenome.Ecoli.NCBI.20080805_1.3.17 multtest_2.8.0
[13] Biobase_2.12.2 biomaRt_2.8.1
[15] chipseq_1.2.0 BSgenome_1.20.0
[17] ShortRead_1.10.4 Rsamtools_1.4.2
[19] lattice_0.19-30 Biostrings_2.20.1
[21] GenomicRanges_1.4.6 IRanges_1.10.4
loaded via a namespace (and not attached):
[1] grid_2.13.1 hwriter_1.2 MASS_7.3-13
RCurl_1.4-2
[5] rtracklayer_1.12.4 splines_2.13.1 survival_2.36-9
tools_2.13.1
[9] XML_3.1-0
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt
[[alternative HTML version deleted]]
Hi Andreia,
On the line "IRanges_JKA<-ranges(Granges_JKA)", you are converting a
genomicRanges object to an IRanges object. BayesPeak accepts a
RangedData object, as opposed to an IRanges object (in order to retain
chromosome information). Replace
IRanges_JKA<-ranges(Granges_JKA)
with
IRanges_JKA<-as(Granges_JKA, "RangedData")
and it should run properly.
Hope this helps,
Jonathan
P.S. additionally, the line Library(BayesPeak) should be
library(BayesPeak) - you obviously know this, else you wouldn't be
getting the correct sessionInfo(), but I point this out in case
anybody else tries to run the code...
________________________________________
From: Andreia Fonseca [andreia.fonseca@gmail.com]
Sent: 20 July 2011 15:24
To: Jonathan Cairns; bioconductor
Subject: error in bayespeak function
Dear all,
I am analyzing chipseq data and I am trying to use bayespeak package
for peak detection.
The code that I am using is
#call libraries
library(GenomicRanges)
Library(BayesPeak)
library(ShortRead)
library(chipseq)
library(ChIPpeakAnno)
library(multicore)
library(GenomicFeatures)
#read sample JKA
JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique
_forfastq.fastq_SAM", overwrite=TRUE,destination="110402_SN365_B_s_2_s
eq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA<-readBamGappedAlignments(JKA)
IRanges_JKA<-ranges(Granges_JKA)
#read Input JKA
JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM", overwrite=TRUE,destination="110402_SN365_B_s_2
_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA_I<-readBamGappedAlignments(JKA_I)
IRanges_JKA_I<-ranges(Granges_JKA_I)
#Peak Calling with BayesPeak
raw.output <- bayespeak(treatment=JKA, control=JKA_I,use.multicore =
TRUE, mc.cores = 4)
after the last command I am getting the forllowing error:
Error in substring(temp[1], 1, 5) : invalid multibyte string at '<ed>'
I also tried to remove the use of parallelization but the error
remains the same, can someone tell me what I am doing wrong ?
thanks for the help,
Andreia
bellow is the information concerning sessionInfo
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BayesPeak_1.4.0 GenomicFeatures_1.4.3
[3] multicore_0.1-5 ChIPpeakAnno_1.8.0
[5] limma_3.8.2 org.Hs.eg.db_2.5.0
[7] GO.db_2.4.1 RSQLite_0.9-1
[9] DBI_0.2-5 AnnotationDbi_1.14.1
[11] BSgenome.Ecoli.NCBI.20080805_1.3.17 multtest_2.8.0
[13] Biobase_2.12.2 biomaRt_2.8.1
[15] chipseq_1.2.0 BSgenome_1.20.0
[17] ShortRead_1.10.4 Rsamtools_1.4.2
[19] lattice_0.19-30 Biostrings_2.20.1
[21] GenomicRanges_1.4.6 IRanges_1.10.4
loaded via a namespace (and not attached):
[1] grid_2.13.1 hwriter_1.2 MASS_7.3-13
RCurl_1.4-2
[5] rtracklayer_1.12.4 splines_2.13.1 survival_2.36-9
tools_2.13.1
[9] XML_3.1-0
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral at fm.ul.pt<mailto:email%3aandreiaamaral at="" fm.ul.pt=""> ; andreiaamaral at fc.ul.pt<mailto:andreiaamaral at="" fc.ul.pt="">
NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for
...{{dropped:16}}
Hi Jonathan,
thanks for the help, I have another error now! I have changed the code
as
you suggested and I also spotted that in bayespeak I was calling the
bam
object instead of the IRanges object, still the IRanges object is not
proper
as you mentioned. I manage to create a RangeData object but :
#call libraries
library(GenomicRanges)
library(BayesPeak)
library(ShortRead)
library(chipseq)
library(ChIPpeakAnno)
library(multicore)
library(GenomicFeatures)
#read sample JKA
JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique
_forfastq.fastq_SAM",
overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_fil
tered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA<-readBamGappedAlignments(JKA)
GIRanges_JKA<-as(Granges_JKA, "GRanges")
IRanges_JKA<-as(GIRanges_JKA, "RangedData")
#read Input JKA
JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM",
overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_fil
tered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA_I<-readBamGappedAlignments(JKA_I)
GIRanges_JKA_I<-as(Granges_JKA_I, "GRanges")
IRanges_JKA_I<-as(GIRanges_JKA_I, "RangedData")
#Peak Calling with BayesPeak
raw.output <- bayespeak(treatment=IRanges_JKA,
control=IRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
error message
Error in `[.default`(space(bed), sel) : invalid subscript type 'S4'
any idea?
thanks
On Wed, Jul 20, 2011 at 3:38 PM, Jonathan Cairns <
Jonathan.Cairns@cancer.org.uk> wrote:
> Hi Andreia,
>
> On the line "IRanges_JKA<-ranges(Granges_JKA)", you are converting a
> genomicRanges object to an IRanges object. BayesPeak accepts a
RangedData
> object, as opposed to an IRanges object (in order to retain
chromosome
> information). Replace
>
> IRanges_JKA<-ranges(Granges_JKA)
>
> with
>
> IRanges_JKA<-as(Granges_JKA, "RangedData")
>
> and it should run properly.
>
> Hope this helps,
>
> Jonathan
>
>
> P.S. additionally, the line Library(BayesPeak) should be
library(BayesPeak)
> - you obviously know this, else you wouldn't be getting the correct
> sessionInfo(), but I point this out in case anybody else tries to
run the
> code...
>
> ________________________________________
> From: Andreia Fonseca [andreia.fonseca@gmail.com]
> Sent: 20 July 2011 15:24
> To: Jonathan Cairns; bioconductor
> Subject: error in bayespeak function
>
> Dear all,
>
> I am analyzing chipseq data and I am trying to use bayespeak package
for
> peak detection.
> The code that I am using is
>
> #call libraries
> library(GenomicRanges)
> Library(BayesPeak)
> library(ShortRead)
> library(chipseq)
> library(ChIPpeakAnno)
> library(multicore)
> library(GenomicFeatures)
>
> #read sample JKA
> JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM",
> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_f
iltered.txt_unique_forfastq.fastq_SAM_BAM")
> Granges_JKA<-readBamGappedAlignments(JKA)
> IRanges_JKA<-ranges(Granges_JKA)
>
> #read Input JKA
> JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_un
ique_forfastq.fastq_SAM",
> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_f
iltered.txt_unique_forfastq.fastq_SAM_BAM")
> Granges_JKA_I<-readBamGappedAlignments(JKA_I)
> IRanges_JKA_I<-ranges(Granges_JKA_I)
>
> #Peak Calling with BayesPeak
> raw.output <- bayespeak(treatment=JKA, control=JKA_I,use.multicore =
TRUE,
> mc.cores = 4)
>
> after the last command I am getting the forllowing error:
> Error in substring(temp[1], 1, 5) : invalid multibyte string at
'<ed>'
>
> I also tried to remove the use of parallelization but the error
remains the
> same, can someone tell me what I am doing wrong ?
> thanks for the help,
> Andreia
>
> bellow is the information concerning sessionInfo
>
> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BayesPeak_1.4.0 GenomicFeatures_1.4.3
> [3] multicore_0.1-5 ChIPpeakAnno_1.8.0
> [5] limma_3.8.2 org.Hs.eg.db_2.5.0
> [7] GO.db_2.4.1 RSQLite_0.9-1
> [9] DBI_0.2-5 AnnotationDbi_1.14.1
> [11] BSgenome.Ecoli.NCBI.20080805_1.3.17 multtest_2.8.0
> [13] Biobase_2.12.2 biomaRt_2.8.1
> [15] chipseq_1.2.0 BSgenome_1.20.0
> [17] ShortRead_1.10.4 Rsamtools_1.4.2
> [19] lattice_0.19-30 Biostrings_2.20.1
> [21] GenomicRanges_1.4.6 IRanges_1.10.4
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.1 hwriter_1.2 MASS_7.3-13
RCurl_1.4-2
> [5] rtracklayer_1.12.4 splines_2.13.1 survival_2.36-9
tools_2.13.1
> [9] XML_3.1-0
>
>
> --
>
> --------------------------------------------------------------------
-------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative
Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral@fm.ul.pt<mailto:email%3aandreiaamaral@fm.ul.pt>
;
> andreiaamaral@fc.ul.pt<mailto:andreiaamaral@fc.ul.pt>
>
>
> NOTICE AND DISCLAIMER
> This e-mail (including any attachments) is intended
fo...{{dropped:31}}
Dear Jonathan,
Maybe it helps to see that my both sample and input information are
now
effectively RangedData objects
IRanges_JKA
RangedData with 3850192 rows and 1 value column across 25 spaces
space ranges | strand
<factor> <iranges> | <rle>
1 chr1 [10071, 10120] | +
2 chr1 [10074, 10123] | +
3 chr1 [10075, 10124] | +
4 chr1 [10075, 10124] | -
5 chr1 [10106, 10155] | -
6 chr1 [10147, 10196] | -
7 chr1 [10148, 10197] | +
8 chr1 [10149, 10198] | +
9 chr1 [10150, 10199] | +
... ... ... ... ...
3850184 chrM [16491, 16540] | -
3850185 chrM [16496, 16545] | -
3850186 chrM [16499, 16548] | +
3850187 chrM [16502, 16551] | +
3850188 chrM [16506, 16555] | -
3850189 chrM [16507, 16556] | +
3850190 chrM [16515, 16564] | -
3850191 chrM [16516, 16565] | -
3850192 chrM [16521, 16570] | +
IRanges_JKA_I
RangedData with 6443227 rows and 1 value column across 25 spaces
space ranges | strand
<factor> <iranges> | <rle>
1 chr1 [10073, 10122] | -
2 chr1 [10165, 10214] | +
3 chr1 [10445, 10494] | +
4 chr1 [13064, 13113] | +
5 chr1 [16060, 16109] | +
6 chr1 [16416, 16465] | -
7 chr1 [20103, 20152] | +
8 chr1 [20103, 20152] | +
9 chr1 [51428, 51477] | -
... ... ... ... ...
6443219 chrM [16509, 16558] | +
6443220 chrM [16511, 16560] | -
6443221 chrM [16512, 16561] | +
6443222 chrM [16513, 16562] | -
6443223 chrM [16516, 16565] | +
6443224 chrM [16516, 16565] | -
6443225 chrM [16517, 16566] | +
6443226 chrM [16518, 16567] | -
6443227 chrM [16520, 16569] | -
On Wed, Jul 20, 2011 at 4:00 PM, Andreia Fonseca
<andreia.fonseca@gmail.com>wrote:
> Hi Jonathan,
>
> thanks for the help, I have another error now! I have changed the
code as
> you suggested and I also spotted that in bayespeak I was calling the
bam
> object instead of the IRanges object, still the IRanges object is
not proper
> as you mentioned. I manage to create a RangeData object but :
>
>
> #call libraries
> library(GenomicRanges)
> library(BayesPeak)
> library(ShortRead)
> library(chipseq)
> library(ChIPpeakAnno)
> library(multicore)
> library(GenomicFeatures)
>
> #read sample JKA
> JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM",
> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_f
iltered.txt_unique_forfastq.fastq_SAM_BAM")
> Granges_JKA<-readBamGappedAlignments(JKA)
> GIRanges_JKA<-as(Granges_JKA, "GRanges")
> IRanges_JKA<-as(GIRanges_JKA, "RangedData")
>
>
> #read Input JKA
> JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_un
ique_forfastq.fastq_SAM",
> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_f
iltered.txt_unique_forfastq.fastq_SAM_BAM")
> Granges_JKA_I<-readBamGappedAlignments(JKA_I)
> GIRanges_JKA_I<-as(Granges_JKA_I, "GRanges")
> IRanges_JKA_I<-as(GIRanges_JKA_I, "RangedData")
>
>
> #Peak Calling with BayesPeak
> raw.output <- bayespeak(treatment=IRanges_JKA,
> control=IRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
>
> error message
>
> Error in `[.default`(space(bed), sel) : invalid subscript type 'S4'
>
> any idea?
> thanks
>
>
>
>
> On Wed, Jul 20, 2011 at 3:38 PM, Jonathan Cairns <
> Jonathan.Cairns@cancer.org.uk> wrote:
>
>> Hi Andreia,
>>
>> On the line "IRanges_JKA<-ranges(Granges_JKA)", you are converting
a
>> genomicRanges object to an IRanges object. BayesPeak accepts a
RangedData
>> object, as opposed to an IRanges object (in order to retain
chromosome
>> information). Replace
>>
>> IRanges_JKA<-ranges(Granges_JKA)
>>
>> with
>>
>> IRanges_JKA<-as(Granges_JKA, "RangedData")
>>
>> and it should run properly.
>>
>> Hope this helps,
>>
>> Jonathan
>>
>>
>> P.S. additionally, the line Library(BayesPeak) should be
>> library(BayesPeak) - you obviously know this, else you wouldn't be
getting
>> the correct sessionInfo(), but I point this out in case anybody
else tries
>> to run the code...
>>
>> ________________________________________
>> From: Andreia Fonseca [andreia.fonseca@gmail.com]
>> Sent: 20 July 2011 15:24
>> To: Jonathan Cairns; bioconductor
>> Subject: error in bayespeak function
>>
>> Dear all,
>>
>> I am analyzing chipseq data and I am trying to use bayespeak
package for
>> peak detection.
>> The code that I am using is
>>
>> #call libraries
>> library(GenomicRanges)
>> Library(BayesPeak)
>> library(ShortRead)
>> library(chipseq)
>> library(ChIPpeakAnno)
>> library(multicore)
>> library(GenomicFeatures)
>>
>> #read sample JKA
>> JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_uni
que_forfastq.fastq_SAM",
>> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_
filtered.txt_unique_forfastq.fastq_SAM_BAM")
>> Granges_JKA<-readBamGappedAlignments(JKA)
>> IRanges_JKA<-ranges(Granges_JKA)
>>
>> #read Input JKA
>> JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_u
nique_forfastq.fastq_SAM",
>> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_
filtered.txt_unique_forfastq.fastq_SAM_BAM")
>> Granges_JKA_I<-readBamGappedAlignments(JKA_I)
>> IRanges_JKA_I<-ranges(Granges_JKA_I)
>>
>> #Peak Calling with BayesPeak
>> raw.output <- bayespeak(treatment=JKA, control=JKA_I,use.multicore
= TRUE,
>> mc.cores = 4)
>>
>> after the last command I am getting the forllowing error:
>> Error in substring(temp[1], 1, 5) : invalid multibyte string at
'<ed>'
>>
>> I also tried to remove the use of parallelization but the error
remains
>> the same, can someone tell me what I am doing wrong ?
>> thanks for the help,
>> Andreia
>>
>> bellow is the information concerning sessionInfo
>>
>> sessionInfo()
>> R version 2.13.1 (2011-07-08)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods
base
>>
>> other attached packages:
>> [1] BayesPeak_1.4.0 GenomicFeatures_1.4.3
>> [3] multicore_0.1-5 ChIPpeakAnno_1.8.0
>> [5] limma_3.8.2 org.Hs.eg.db_2.5.0
>> [7] GO.db_2.4.1 RSQLite_0.9-1
>> [9] DBI_0.2-5 AnnotationDbi_1.14.1
>> [11] BSgenome.Ecoli.NCBI.20080805_1.3.17 multtest_2.8.0
>> [13] Biobase_2.12.2 biomaRt_2.8.1
>> [15] chipseq_1.2.0 BSgenome_1.20.0
>> [17] ShortRead_1.10.4 Rsamtools_1.4.2
>> [19] lattice_0.19-30 Biostrings_2.20.1
>> [21] GenomicRanges_1.4.6 IRanges_1.10.4
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.13.1 hwriter_1.2 MASS_7.3-13
RCurl_1.4-2
>> [5] rtracklayer_1.12.4 splines_2.13.1 survival_2.36-9
tools_2.13.1
>> [9] XML_3.1-0
>>
>>
>> --
>>
>> -------------------------------------------------------------------
--------------------------
>> Andreia J. Amaral, PhD
>> BioFIG - Center for Biodiversity, Functional and Integrative
Genomics
>> Instituto de Medicina Molecular
>> University of Lisbon
>> Tel: +352 217500000 (ext. office: 28253)
>> email:andreiaamaral@fm.ul.pt<mailto:email%3aandreiaamaral@fm.ul.pt>
;
>> andreiaamaral@fc.ul.pt<mailto:andreiaamaral@fc.ul.pt>
>>
>>
>> NOTICE AND DISCLAIMER
>> This e-mail (including any attachments) is intended for the above-
named
>> person(s). If you are not the intended recipient, notify the sender
>> immediately, delete this email from your system and do not disclose
or use
>> for any purpose.
>>
>> We may monitor all incoming and outgoing emails in line with
current
>> legislation. We have taken steps to ensure that this email and
attachments
>> are free from any virus, but it remains your responsibility to
ensure that
>> viruses do not adversely affect you.
>> Cancer Research UK
>> Registered in England and Wales
>> Company Registered Number: 4325234.
>> Registered Charity Number: 1089464 and Scotland SC041666
>> Registered Office Address: Angel Building, 407 St John Street,
London EC1V
>> 4AD.
>>
>
>
>
> --
>
> --------------------------------------------------------------------
-------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative
Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt
>
>
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt
[[alternative HTML version deleted]]
Andreia,
That's very strange. What happens when you do:
str(space(GIRanges_JKA))
str(space(GIRanges_JKA_I))
Do either of these result in an error?
You could try attaching the package rtracklayer at the start; I find
that this sometimes fixes odd IRanges behaviour.
Jonathan
________________________________________
From: Andreia Fonseca [andreia.fonseca@gmail.com]
Sent: 20 July 2011 17:11
To: Jonathan Cairns
Cc: bioconductor
Subject: Re: error in bayespeak function
Dear Jonathan,
Maybe it helps to see that my both sample and input information are
now effectively RangedData objects
IRanges_JKA
RangedData with 3850192 rows and 1 value column across 25 spaces
space ranges | strand
<factor> <iranges> | <rle>
1 chr1 [10071, 10120] | +
2 chr1 [10074, 10123] | +
3 chr1 [10075, 10124] | +
4 chr1 [10075, 10124] | -
5 chr1 [10106, 10155] | -
6 chr1 [10147, 10196] | -
7 chr1 [10148, 10197] | +
8 chr1 [10149, 10198] | +
9 chr1 [10150, 10199] | +
... ... ... ... ...
3850184 chrM [16491, 16540] | -
3850185 chrM [16496, 16545] | -
3850186 chrM [16499, 16548] | +
3850187 chrM [16502, 16551] | +
3850188 chrM [16506, 16555] | -
3850189 chrM [16507, 16556] | +
3850190 chrM [16515, 16564] | -
3850191 chrM [16516, 16565] | -
3850192 chrM [16521, 16570] | +
IRanges_JKA_I
RangedData with 6443227 rows and 1 value column across 25 spaces
space ranges | strand
<factor> <iranges> | <rle>
1 chr1 [10073, 10122] | -
2 chr1 [10165, 10214] | +
3 chr1 [10445, 10494] | +
4 chr1 [13064, 13113] | +
5 chr1 [16060, 16109] | +
6 chr1 [16416, 16465] | -
7 chr1 [20103, 20152] | +
8 chr1 [20103, 20152] | +
9 chr1 [51428, 51477] | -
... ... ... ... ...
6443219 chrM [16509, 16558] | +
6443220 chrM [16511, 16560] | -
6443221 chrM [16512, 16561] | +
6443222 chrM [16513, 16562] | -
6443223 chrM [16516, 16565] | +
6443224 chrM [16516, 16565] | -
6443225 chrM [16517, 16566] | +
6443226 chrM [16518, 16567] | -
6443227 chrM [16520, 16569] | -
On Wed, Jul 20, 2011 at 4:00 PM, Andreia Fonseca <andreia.fonseca at="" gmail.com<mailto:andreia.fonseca="" at="" gmail.com="">> wrote:
Hi Jonathan,
thanks for the help, I have another error now! I have changed the code
as you suggested and I also spotted that in bayespeak I was calling
the bam object instead of the IRanges object, still the IRanges object
is not proper as you mentioned. I manage to create a RangeData object
but :
#call libraries
library(GenomicRanges)
library(BayesPeak)
library(ShortRead)
library(chipseq)
library(ChIPpeakAnno)
library(multicore)
library(GenomicFeatures)
#read sample JKA
JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique
_forfastq.fastq_SAM", overwrite=TRUE,destination="110402_SN365_B_s_2_s
eq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA<-readBamGappedAlignments(JKA)
GIRanges_JKA<-as(Granges_JKA, "GRanges")
IRanges_JKA<-as(GIRanges_JKA, "RangedData")
#read Input JKA
JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM", overwrite=TRUE,destination="110402_SN365_B_s_2
_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA_I<-readBamGappedAlignments(JKA_I)
GIRanges_JKA_I<-as(Granges_JKA_I, "GRanges")
IRanges_JKA_I<-as(GIRanges_JKA_I, "RangedData")
#Peak Calling with BayesPeak
raw.output <- bayespeak(treatment=IRanges_JKA,
control=IRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
error message
Error in `[.default`(space(bed), sel) : invalid subscript type 'S4'
any idea?
thanks
On Wed, Jul 20, 2011 at 3:38 PM, Jonathan Cairns <jonathan.cairns at="" cancer.org.uk<mailto:jonathan.cairns="" at="" cancer.org.uk="">> wrote:
Hi Andreia,
On the line "IRanges_JKA<-ranges(Granges_JKA)", you are converting a
genomicRanges object to an IRanges object. BayesPeak accepts a
RangedData object, as opposed to an IRanges object (in order to retain
chromosome information). Replace
IRanges_JKA<-ranges(Granges_JKA)
with
IRanges_JKA<-as(Granges_JKA, "RangedData")
and it should run properly.
Hope this helps,
Jonathan
P.S. additionally, the line Library(BayesPeak) should be
library(BayesPeak) - you obviously know this, else you wouldn't be
getting the correct sessionInfo(), but I point this out in case
anybody else tries to run the code...
________________________________________
From: Andreia Fonseca
[andreia.fonseca@gmail.com<mailto:andreia.fonseca@gmail.com>]
Sent: 20 July 2011 15:24
To: Jonathan Cairns; bioconductor
Subject: error in bayespeak function
Dear all,
I am analyzing chipseq data and I am trying to use bayespeak package
for peak detection.
The code that I am using is
#call libraries
library(GenomicRanges)
Library(BayesPeak)
library(ShortRead)
library(chipseq)
library(ChIPpeakAnno)
library(multicore)
library(GenomicFeatures)
#read sample JKA
JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique
_forfastq.fastq_SAM", overwrite=TRUE,destination="110402_SN365_B_s_2_s
eq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA<-readBamGappedAlignments(JKA)
IRanges_JKA<-ranges(Granges_JKA)
#read Input JKA
JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM", overwrite=TRUE,destination="110402_SN365_B_s_2
_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA_I<-readBamGappedAlignments(JKA_I)
IRanges_JKA_I<-ranges(Granges_JKA_I)
#Peak Calling with BayesPeak
raw.output <- bayespeak(treatment=JKA, control=JKA_I,use.multicore =
TRUE, mc.cores = 4)
after the last command I am getting the forllowing error:
Error in substring(temp[1], 1, 5) : invalid multibyte string at '<ed>'
I also tried to remove the use of parallelization but the error
remains the same, can someone tell me what I am doing wrong ?
thanks for the help,
Andreia
bellow is the information concerning sessionInfo
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BayesPeak_1.4.0 GenomicFeatures_1.4.3
[3] multicore_0.1-5 ChIPpeakAnno_1.8.0
[5] limma_3.8.2 org.Hs.eg.db_2.5.0
[7] GO.db_2.4.1 RSQLite_0.9-1
[9] DBI_0.2-5 AnnotationDbi_1.14.1
[11] BSgenome.Ecoli.NCBI.20080805_1.3.17 multtest_2.8.0
[13] Biobase_2.12.2 biomaRt_2.8.1
[15] chipseq_1.2.0 BSgenome_1.20.0
[17] ShortRead_1.10.4 Rsamtools_1.4.2
[19] lattice_0.19-30 Biostrings_2.20.1
[21] GenomicRanges_1.4.6 IRanges_1.10.4
loaded via a namespace (and not attached):
[1] grid_2.13.1 hwriter_1.2 MASS_7.3-13
RCurl_1.4-2
[5] rtracklayer_1.12.4 splines_2.13.1 survival_2.36-9
tools_2.13.1
[9] XML_3.1-0
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral at fm.ul.pt<mailto:email%3aandreiaamaral at="" fm.ul.pt=""><mailto:email%3aandreiaamaral at="" fm.ul.pt<mailto:email%253aandreiaamaral="" at="" fm.ul.pt="">> ; andreiaamaral
at fc.ul.pt<mailto:andreiaamaral at="" fc.ul.pt=""><mailto:andreiaamaral at="" fc.ul.pt<mailto:andreiaamaral="" at="" fc.ul.pt="">>
NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for the above-
named person(s). If you are not the intended recipient, notify the
sender immediately, delete this email from your system and do not
disclose or use for any purpose.
We may monitor all incoming and outgoing emails in line with current
legislation. We have taken steps to ensure that this email and
attachments are free from any virus, but it remains your
responsibility to ensure that viruses do not adversely affect you.
Cancer Research UK
Registered in England and Wales
Company Registered Number: 4325234.
Registered Charity Number: 1089464 and Scotland SC041666
Registered Office Address: Angel Building, 407 St John Street, London
EC1V 4AD.
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral at fm.ul.pt<mailto:email%3aandreiaamaral at="" fm.ul.pt=""> ; andreiaamaral at fc.ul.pt<mailto:andreiaamaral at="" fc.ul.pt="">
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral at fm.ul.pt<mailto:email%3aandreiaamaral at="" fm.ul.pt=""> ; andreiaamaral at fc.ul.pt<mailto:andreiaamaral at="" fc.ul.pt="">
NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for the above-
named person(s). If you are not the intended recipient, notify the
sender immediately, delete this email from your system and do not
disclose or use for any purpose.
We may monitor all incoming and outgoing emails in line with current
legislation. We have taken steps to ensure that this email and
attachments are free from any virus, but it remains your
responsibility to ensure that viruses do not adversely affect you.
Cancer Research UK
Registered in England and Wales
Company Registered Number: 4325234.
Registered Charity Number: 1089464 and Scotland SC041666
Registered Office Address: Angel Building, 407 St John Street, London
EC1V 4AD.
Hi Jonathan,
after doing str(space(GIRanges_JKA)) and str(space(GIRanges_JKA_I))
it results in the following error:
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "space", for
signature
"GRanges"
I have attached rtracklayer as you suggested and run the code again
and now
the error meassage has changed, it seems is not being able to find the
strand information
raw.output <- bayespeak(treatment=GIRanges_JKA,
control=GIRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
Error in bed$strand : $ operator not defined for this S4 class
one other thing that I did was to use the example data that you
provide
sig <- read.table("H3K4me3-chr16.bed", skip=1,
colClasses=c("character",
"numeric")[c(1,2,2,1,1,1,1,1,1)])
bgr <- read.table("Input-chr16.bed", colClasses=c("character",
"numeric")[c(1,2,2,1,1,1,1,1,1)])
sig <- RangedData(space=sig[,1], IRanges(start=sig[,2], end=sig[,3]),
strand=sig[,6])
bgr <- RangedData(space=bgr[,1], IRanges(start=bgr[,2], end=bgr[,3]),
strand=bgr[,6])> bgr <- read.table("Input-chr16.bed",
colClasses=c("character", "numeric")
and then I do not get an error when running bayespeak...
On Wed, Jul 20, 2011 at 5:49 PM, Jonathan Cairns <
Jonathan.Cairns@cancer.org.uk> wrote:
> Andreia,
>
> That's very strange. What happens when you do:
>
> str(space(GIRanges_JKA))
> str(space(GIRanges_JKA_I))
>
> Do either of these result in an error?
>
> You could try attaching the package rtracklayer at the start; I find
that
> this sometimes fixes odd IRanges behaviour.
>
> Jonathan
> ________________________________________
> From: Andreia Fonseca [andreia.fonseca@gmail.com]
> Sent: 20 July 2011 17:11
> To: Jonathan Cairns
> Cc: bioconductor
> Subject: Re: error in bayespeak function
>
> Dear Jonathan,
>
> Maybe it helps to see that my both sample and input information are
now
> effectively RangedData objects
>
> IRanges_JKA
> RangedData with 3850192 rows and 1 value column across 25 spaces
> space ranges | strand
> <factor> <iranges> | <rle>
> 1 chr1 [10071, 10120] | +
> 2 chr1 [10074, 10123] | +
> 3 chr1 [10075, 10124] | +
> 4 chr1 [10075, 10124] | -
> 5 chr1 [10106, 10155] | -
> 6 chr1 [10147, 10196] | -
> 7 chr1 [10148, 10197] | +
> 8 chr1 [10149, 10198] | +
> 9 chr1 [10150, 10199] | +
> ... ... ... ... ...
> 3850184 chrM [16491, 16540] | -
> 3850185 chrM [16496, 16545] | -
> 3850186 chrM [16499, 16548] | +
> 3850187 chrM [16502, 16551] | +
> 3850188 chrM [16506, 16555] | -
> 3850189 chrM [16507, 16556] | +
> 3850190 chrM [16515, 16564] | -
> 3850191 chrM [16516, 16565] | -
> 3850192 chrM [16521, 16570] | +
>
> IRanges_JKA_I
> RangedData with 6443227 rows and 1 value column across 25 spaces
> space ranges | strand
> <factor> <iranges> | <rle>
> 1 chr1 [10073, 10122] | -
> 2 chr1 [10165, 10214] | +
> 3 chr1 [10445, 10494] | +
> 4 chr1 [13064, 13113] | +
> 5 chr1 [16060, 16109] | +
> 6 chr1 [16416, 16465] | -
> 7 chr1 [20103, 20152] | +
> 8 chr1 [20103, 20152] | +
> 9 chr1 [51428, 51477] | -
> ... ... ... ... ...
> 6443219 chrM [16509, 16558] | +
> 6443220 chrM [16511, 16560] | -
> 6443221 chrM [16512, 16561] | +
> 6443222 chrM [16513, 16562] | -
> 6443223 chrM [16516, 16565] | +
> 6443224 chrM [16516, 16565] | -
> 6443225 chrM [16517, 16566] | +
> 6443226 chrM [16518, 16567] | -
> 6443227 chrM [16520, 16569] | -
>
>
> On Wed, Jul 20, 2011 at 4:00 PM, Andreia Fonseca <
> andreia.fonseca@gmail.com<mailto:andreia.fonseca@gmail.com>> wrote:
> Hi Jonathan,
>
> thanks for the help, I have another error now! I have changed the
code as
> you suggested and I also spotted that in bayespeak I was calling the
bam
> object instead of the IRanges object, still the IRanges object is
not proper
> as you mentioned. I manage to create a RangeData object but :
>
>
> #call libraries
> library(GenomicRanges)
> library(BayesPeak)
> library(ShortRead)
> library(chipseq)
> library(ChIPpeakAnno)
> library(multicore)
> library(GenomicFeatures)
>
> #read sample JKA
> JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM",
> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_f
iltered.txt_unique_forfastq.fastq_SAM_BAM")
> Granges_JKA<-readBamGappedAlignments(JKA)
> GIRanges_JKA<-as(Granges_JKA, "GRanges")
> IRanges_JKA<-as(GIRanges_JKA, "RangedData")
>
>
> #read Input JKA
> JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_un
ique_forfastq.fastq_SAM",
> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_f
iltered.txt_unique_forfastq.fastq_SAM_BAM")
> Granges_JKA_I<-readBamGappedAlignments(JKA_I)
> GIRanges_JKA_I<-as(Granges_JKA_I, "GRanges")
> IRanges_JKA_I<-as(GIRanges_JKA_I, "RangedData")
>
>
> #Peak Calling with BayesPeak
> raw.output <- bayespeak(treatment=IRanges_JKA,
> control=IRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
>
> error message
>
> Error in `[.default`(space(bed), sel) : invalid subscript type 'S4'
>
> any idea?
> thanks
>
>
>
>
> On Wed, Jul 20, 2011 at 3:38 PM, Jonathan Cairns <
> Jonathan.Cairns@cancer.org.uk<mailto:jonathan.cairns@cancer.org.uk>>
> wrote:
> Hi Andreia,
>
> On the line "IRanges_JKA<-ranges(Granges_JKA)", you are converting a
> genomicRanges object to an IRanges object. BayesPeak accepts a
RangedData
> object, as opposed to an IRanges object (in order to retain
chromosome
> information). Replace
>
> IRanges_JKA<-ranges(Granges_JKA)
>
> with
>
> IRanges_JKA<-as(Granges_JKA, "RangedData")
>
> and it should run properly.
>
> Hope this helps,
>
> Jonathan
>
>
> P.S. additionally, the line Library(BayesPeak) should be
library(BayesPeak)
> - you obviously know this, else you wouldn't be getting the correct
> sessionInfo(), but I point this out in case anybody else tries to
run the
> code...
>
> ________________________________________
> From: Andreia Fonseca [andreia.fonseca@gmail.com<mailto:> andreia.fonseca@gmail.com>]
> Sent: 20 July 2011 15:24
> To: Jonathan Cairns; bioconductor
> Subject: error in bayespeak function
>
> Dear all,
>
> I am analyzing chipseq data and I am trying to use bayespeak package
for
> peak detection.
> The code that I am using is
>
> #call libraries
> library(GenomicRanges)
> Library(BayesPeak)
> library(ShortRead)
> library(chipseq)
> library(ChIPpeakAnno)
> library(multicore)
> library(GenomicFeatures)
>
> #read sample JKA
> JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM",
> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_f
iltered.txt_unique_forfastq.fastq_SAM_BAM")
> Granges_JKA<-readBamGappedAlignments(JKA)
> IRanges_JKA<-ranges(Granges_JKA)
>
> #read Input JKA
> JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_un
ique_forfastq.fastq_SAM",
> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_f
iltered.txt_unique_forfastq.fastq_SAM_BAM")
> Granges_JKA_I<-readBamGappedAlignments(JKA_I)
> IRanges_JKA_I<-ranges(Granges_JKA_I)
>
> #Peak Calling with BayesPeak
> raw.output <- bayespeak(treatment=JKA, control=JKA_I,use.multicore =
TRUE,
> mc.cores = 4)
>
> after the last command I am getting the forllowing error:
> Error in substring(temp[1], 1, 5) : invalid multibyte string at
'<ed>'
>
> I also tried to remove the use of parallelization but the error
remains the
> same, can someone tell me what I am doing wrong ?
> thanks for the help,
> Andreia
>
> bellow is the information concerning sessionInfo
>
> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BayesPeak_1.4.0 GenomicFeatures_1.4.3
> [3] multicore_0.1-5 ChIPpeakAnno_1.8.0
> [5] limma_3.8.2 org.Hs.eg.db_2.5.0
> [7] GO.db_2.4.1 RSQLite_0.9-1
> [9] DBI_0.2-5 AnnotationDbi_1.14.1
> [11] BSgenome.Ecoli.NCBI.20080805_1.3.17 multtest_2.8.0
> [13] Biobase_2.12.2 biomaRt_2.8.1
> [15] chipseq_1.2.0 BSgenome_1.20.0
> [17] ShortRead_1.10.4 Rsamtools_1.4.2
> [19] lattice_0.19-30 Biostrings_2.20.1
> [21] GenomicRanges_1.4.6 IRanges_1.10.4
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.1 hwriter_1.2 MASS_7.3-13
RCurl_1.4-2
> [5] rtracklayer_1.12.4 splines_2.13.1 survival_2.36-9
tools_2.13.1
> [9] XML_3.1-0
>
>
> --
>
> --------------------------------------------------------------------
-------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative
Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral@fm.ul.pt<mailto:email%3aandreiaamaral@fm.ul.pt> ><mailto:email%3aandreiaamaral@fm.ul.pt<mailto:> email%253Aandreiaamaral@fm.ul.pt>> ; andreiaamaral@fc.ul.pt<mailto:> andreiaamaral@fc.ul.pt><mailto:andreiaamaral@fc.ul.pt<mailto:> andreiaamaral@fc.ul.pt>>
>
>
> NOTICE AND DISCLAIMER
> This e-mail (including any attachments) is intended for the above-
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> immediately, delete this email from your system and do not disclose
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> We may monitor all incoming and outgoing emails in line with current
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> Registered Charity Number: 1089464 and Scotland SC041666
> Registered Office Address: Angel Building, 407 St John Street,
London EC1V
> 4AD.
>
>
>
> --
>
> --------------------------------------------------------------------
-------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative
Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral@fm.ul.pt<mailto:email%3aandreiaamaral@fm.ul.pt>
;
> andreiaamaral@fc.ul.pt<mailto:andreiaamaral@fc.ul.pt>
>
>
>
>
> --
>
> --------------------------------------------------------------------
-------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative
Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral@fm.ul.pt<mailto:email%3aandreiaamaral@fm.ul.pt>
;
> andreiaamaral@fc.ul.pt<mailto:andreiaamaral@fc.ul.pt>
>
>
> NOTICE AND DISCLAIMER
> This e-mail (including any attachments) is intended for the above-
named
> person(s). If you are not the intended recipient, notify the sender
> immediately, delete this email from your system and do not disclose
or use
> for any purpose.
>
> We may monitor all incoming and outgoing emails in line with current
> legislation. We have taken steps to ensure that this email and
attachments
> are free from any virus, but it remains your responsibility to
ensure that
> viruses do not adversely affect you.
> Cancer Research UK
> Registered in England and Wales
> Company Registered Number: 4325234.
> Registered Charity Number: 1089464 and Scotland SC041666
> Registered Office Address: Angel Building, 407 St John Street,
London EC1V
> 4AD.
>
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt
[[alternative HTML version deleted]]
sorry, please disregard my last email. The RangedData is the object
IRanges_JKA_I and IRanges_JKA,
the error remains the same, it does not cahnge after attaching
rtracklayer
raw.output <- bayespeak(treatment=IRanges_JKA,
control=IRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
Error in `[.default`(space(bed), sel) : invalid subscript type 'S4'
after making
str(space(IRanges_JKA_I))
Factor w/ 25 levels "chr1","chr2",..: 1 1 1 1 1 1 1 1 1 1 ...
str(space(IRanges_JKA))
Factor w/ 25 levels "chr1","chr2",..: 1 1 1 1 1 1 1 1 1 1 ...
On Wed, Jul 20, 2011 at 6:06 PM, Andreia Fonseca
<andreia.fonseca@gmail.com>wrote:
> Hi Jonathan,
>
> after doing str(space(GIRanges_JKA)) and str(space(GIRanges_JKA_I))
> it results in the following error:
>
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "space", for
signature
> "GRanges"
>
> I have attached rtracklayer as you suggested and run the code again
and now
> the error meassage has changed, it seems is not being able to find
the
> strand information
>
> raw.output <- bayespeak(treatment=GIRanges_JKA,
> control=GIRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
> Error in bed$strand : $ operator not defined for this S4 class
>
> one other thing that I did was to use the example data that you
provide
> sig <- read.table("H3K4me3-chr16.bed", skip=1,
colClasses=c("character",
> "numeric")[c(1,2,2,1,1,1,1,1,1)])
> bgr <- read.table("Input-chr16.bed", colClasses=c("character",
> "numeric")[c(1,2,2,1,1,1,1,1,1)])
> sig <- RangedData(space=sig[,1], IRanges(start=sig[,2],
end=sig[,3]),
> strand=sig[,6])
> bgr <- RangedData(space=bgr[,1], IRanges(start=bgr[,2],
end=bgr[,3]),
> strand=bgr[,6])> bgr <- read.table("Input-chr16.bed",
> colClasses=c("character", "numeric")
>
> and then I do not get an error when running bayespeak...
>
>
>
> On Wed, Jul 20, 2011 at 5:49 PM, Jonathan Cairns <
> Jonathan.Cairns@cancer.org.uk> wrote:
>
>> Andreia,
>>
>> That's very strange. What happens when you do:
>>
>> str(space(GIRanges_JKA))
>> str(space(GIRanges_JKA_I))
>>
>> Do either of these result in an error?
>>
>> You could try attaching the package rtracklayer at the start; I
find that
>> this sometimes fixes odd IRanges behaviour.
>>
>> Jonathan
>> ________________________________________
>> From: Andreia Fonseca [andreia.fonseca@gmail.com]
>> Sent: 20 July 2011 17:11
>> To: Jonathan Cairns
>> Cc: bioconductor
>> Subject: Re: error in bayespeak function
>>
>> Dear Jonathan,
>>
>> Maybe it helps to see that my both sample and input information are
now
>> effectively RangedData objects
>>
>> IRanges_JKA
>> RangedData with 3850192 rows and 1 value column across 25 spaces
>> space ranges | strand
>> <factor> <iranges> | <rle>
>> 1 chr1 [10071, 10120] | +
>> 2 chr1 [10074, 10123] | +
>> 3 chr1 [10075, 10124] | +
>> 4 chr1 [10075, 10124] | -
>> 5 chr1 [10106, 10155] | -
>> 6 chr1 [10147, 10196] | -
>> 7 chr1 [10148, 10197] | +
>> 8 chr1 [10149, 10198] | +
>> 9 chr1 [10150, 10199] | +
>> ... ... ... ... ...
>> 3850184 chrM [16491, 16540] | -
>> 3850185 chrM [16496, 16545] | -
>> 3850186 chrM [16499, 16548] | +
>> 3850187 chrM [16502, 16551] | +
>> 3850188 chrM [16506, 16555] | -
>> 3850189 chrM [16507, 16556] | +
>> 3850190 chrM [16515, 16564] | -
>> 3850191 chrM [16516, 16565] | -
>> 3850192 chrM [16521, 16570] | +
>>
>> IRanges_JKA_I
>> RangedData with 6443227 rows and 1 value column across 25 spaces
>> space ranges | strand
>> <factor> <iranges> | <rle>
>> 1 chr1 [10073, 10122] | -
>> 2 chr1 [10165, 10214] | +
>> 3 chr1 [10445, 10494] | +
>> 4 chr1 [13064, 13113] | +
>> 5 chr1 [16060, 16109] | +
>> 6 chr1 [16416, 16465] | -
>> 7 chr1 [20103, 20152] | +
>> 8 chr1 [20103, 20152] | +
>> 9 chr1 [51428, 51477] | -
>> ... ... ... ... ...
>> 6443219 chrM [16509, 16558] | +
>> 6443220 chrM [16511, 16560] | -
>> 6443221 chrM [16512, 16561] | +
>> 6443222 chrM [16513, 16562] | -
>> 6443223 chrM [16516, 16565] | +
>> 6443224 chrM [16516, 16565] | -
>> 6443225 chrM [16517, 16566] | +
>> 6443226 chrM [16518, 16567] | -
>> 6443227 chrM [16520, 16569] | -
>>
>>
>> On Wed, Jul 20, 2011 at 4:00 PM, Andreia Fonseca <
>> andreia.fonseca@gmail.com<mailto:andreia.fonseca@gmail.com>> wrote:
>> Hi Jonathan,
>>
>> thanks for the help, I have another error now! I have changed the
code as
>> you suggested and I also spotted that in bayespeak I was calling
the bam
>> object instead of the IRanges object, still the IRanges object is
not proper
>> as you mentioned. I manage to create a RangeData object but :
>>
>>
>> #call libraries
>> library(GenomicRanges)
>> library(BayesPeak)
>> library(ShortRead)
>> library(chipseq)
>> library(ChIPpeakAnno)
>> library(multicore)
>> library(GenomicFeatures)
>>
>> #read sample JKA
>> JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_uni
que_forfastq.fastq_SAM",
>> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_
filtered.txt_unique_forfastq.fastq_SAM_BAM")
>> Granges_JKA<-readBamGappedAlignments(JKA)
>> GIRanges_JKA<-as(Granges_JKA, "GRanges")
>> IRanges_JKA<-as(GIRanges_JKA, "RangedData")
>>
>>
>> #read Input JKA
>> JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_u
nique_forfastq.fastq_SAM",
>> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_
filtered.txt_unique_forfastq.fastq_SAM_BAM")
>> Granges_JKA_I<-readBamGappedAlignments(JKA_I)
>> GIRanges_JKA_I<-as(Granges_JKA_I, "GRanges")
>> IRanges_JKA_I<-as(GIRanges_JKA_I, "RangedData")
>>
>>
>> #Peak Calling with BayesPeak
>> raw.output <- bayespeak(treatment=IRanges_JKA,
>> control=IRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
>>
>> error message
>>
>> Error in `[.default`(space(bed), sel) : invalid subscript type 'S4'
>>
>> any idea?
>> thanks
>>
>>
>>
>>
>> On Wed, Jul 20, 2011 at 3:38 PM, Jonathan Cairns <
>>
Jonathan.Cairns@cancer.org.uk<mailto:jonathan.cairns@cancer.org.uk>>
>> wrote:
>> Hi Andreia,
>>
>> On the line "IRanges_JKA<-ranges(Granges_JKA)", you are converting
a
>> genomicRanges object to an IRanges object. BayesPeak accepts a
RangedData
>> object, as opposed to an IRanges object (in order to retain
chromosome
>> information). Replace
>>
>> IRanges_JKA<-ranges(Granges_JKA)
>>
>> with
>>
>> IRanges_JKA<-as(Granges_JKA, "RangedData")
>>
>> and it should run properly.
>>
>> Hope this helps,
>>
>> Jonathan
>>
>>
>> P.S. additionally, the line Library(BayesPeak) should be
>> library(BayesPeak) - you obviously know this, else you wouldn't be
getting
>> the correct sessionInfo(), but I point this out in case anybody
else tries
>> to run the code...
>>
>> ________________________________________
>> From: Andreia Fonseca [andreia.fonseca@gmail.com<mailto:>> andreia.fonseca@gmail.com>]
>> Sent: 20 July 2011 15:24
>> To: Jonathan Cairns; bioconductor
>> Subject: error in bayespeak function
>>
>> Dear all,
>>
>> I am analyzing chipseq data and I am trying to use bayespeak
package for
>> peak detection.
>> The code that I am using is
>>
>> #call libraries
>> library(GenomicRanges)
>> Library(BayesPeak)
>> library(ShortRead)
>> library(chipseq)
>> library(ChIPpeakAnno)
>> library(multicore)
>> library(GenomicFeatures)
>>
>> #read sample JKA
>> JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_uni
que_forfastq.fastq_SAM",
>> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_
filtered.txt_unique_forfastq.fastq_SAM_BAM")
>> Granges_JKA<-readBamGappedAlignments(JKA)
>> IRanges_JKA<-ranges(Granges_JKA)
>>
>> #read Input JKA
>> JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_u
nique_forfastq.fastq_SAM",
>> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_
filtered.txt_unique_forfastq.fastq_SAM_BAM")
>> Granges_JKA_I<-readBamGappedAlignments(JKA_I)
>> IRanges_JKA_I<-ranges(Granges_JKA_I)
>>
>> #Peak Calling with BayesPeak
>> raw.output <- bayespeak(treatment=JKA, control=JKA_I,use.multicore
= TRUE,
>> mc.cores = 4)
>>
>> after the last command I am getting the forllowing error:
>> Error in substring(temp[1], 1, 5) : invalid multibyte string at
'<ed>'
>>
>> I also tried to remove the use of parallelization but the error
remains
>> the same, can someone tell me what I am doing wrong ?
>> thanks for the help,
>> Andreia
>>
>> bellow is the information concerning sessionInfo
>>
>> sessionInfo()
>> R version 2.13.1 (2011-07-08)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods
base
>>
>> other attached packages:
>> [1] BayesPeak_1.4.0 GenomicFeatures_1.4.3
>> [3] multicore_0.1-5 ChIPpeakAnno_1.8.0
>> [5] limma_3.8.2 org.Hs.eg.db_2.5.0
>> [7] GO.db_2.4.1 RSQLite_0.9-1
>> [9] DBI_0.2-5 AnnotationDbi_1.14.1
>> [11] BSgenome.Ecoli.NCBI.20080805_1.3.17 multtest_2.8.0
>> [13] Biobase_2.12.2 biomaRt_2.8.1
>> [15] chipseq_1.2.0 BSgenome_1.20.0
>> [17] ShortRead_1.10.4 Rsamtools_1.4.2
>> [19] lattice_0.19-30 Biostrings_2.20.1
>> [21] GenomicRanges_1.4.6 IRanges_1.10.4
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.13.1 hwriter_1.2 MASS_7.3-13
RCurl_1.4-2
>> [5] rtracklayer_1.12.4 splines_2.13.1 survival_2.36-9
tools_2.13.1
>> [9] XML_3.1-0
>>
>>
>> --
>>
>> -------------------------------------------------------------------
--------------------------
>> Andreia J. Amaral, PhD
>> BioFIG - Center for Biodiversity, Functional and Integrative
Genomics
>> Instituto de Medicina Molecular
>> University of Lisbon
>> Tel: +352 217500000 (ext. office: 28253)
>> email:andreiaamaral@fm.ul.pt<mailto:email%3aandreiaamaral@fm.ul.pt>> ><mailto:email%3aandreiaamaral@fm.ul.pt<mailto:>> email%253Aandreiaamaral@fm.ul.pt>> ; andreiaamaral@fc.ul.pt<mailto:>> andreiaamaral@fc.ul.pt><mailto:andreiaamaral@fc.ul.pt<mailto:>> andreiaamaral@fc.ul.pt>>
>>
>>
>> NOTICE AND DISCLAIMER
>> This e-mail (including any attachments) is intended for the above-
named
>> person(s). If you are not the intended recipient, notify the sender
>> immediately, delete this email from your system and do not disclose
or use
>> for any purpose.
>>
>> We may monitor all incoming and outgoing emails in line with
current
>> legislation. We have taken steps to ensure that this email and
attachments
>> are free from any virus, but it remains your responsibility to
ensure that
>> viruses do not adversely affect you.
>> Cancer Research UK
>> Registered in England and Wales
>> Company Registered Number: 4325234.
>> Registered Charity Number: 1089464 and Scotland SC041666
>> Registered Office Address: Angel Building, 407 St John Street,
London EC1V
>> 4AD.
>>
>>
>>
>> --
>>
>> -------------------------------------------------------------------
--------------------------
>> Andreia J. Amaral, PhD
>> BioFIG - Center for Biodiversity, Functional and Integrative
Genomics
>> Instituto de Medicina Molecular
>> University of Lisbon
>> Tel: +352 217500000 (ext. office: 28253)
>> email:andreiaamaral@fm.ul.pt<mailto:email%3aandreiaamaral@fm.ul.pt>
;
>> andreiaamaral@fc.ul.pt<mailto:andreiaamaral@fc.ul.pt>
>>
>>
>>
>>
>> --
>>
>> -------------------------------------------------------------------
--------------------------
>> Andreia J. Amaral, PhD
>> BioFIG - Center for Biodiversity, Functional and Integrative
Genomics
>> Instituto de Medicina Molecular
>> University of Lisbon
>> Tel: +352 217500000 (ext. office: 28253)
>> email:andreiaamaral@fm.ul.pt<mailto:email%3aandreiaamaral@fm.ul.pt>
;
>> andreiaamaral@fc.ul.pt<mailto:andreiaamaral@fc.ul.pt>
>>
>>
>> NOTICE AND DISCLAIMER
>> This e-mail (including any attachments) is intended for the above-
named
>> person(s). If you are not the intended recipient, notify the sender
>> immediately, delete this email from your system and do not disclose
or use
>> for any purpose.
>>
>> We may monitor all incoming and outgoing emails in line with
current
>> legislation. We have taken steps to ensure that this email and
attachments
>> are free from any virus, but it remains your responsibility to
ensure that
>> viruses do not adversely affect you.
>> Cancer Research UK
>> Registered in England and Wales
>> Company Registered Number: 4325234.
>> Registered Charity Number: 1089464 and Scotland SC041666
>> Registered Office Address: Angel Building, 407 St John Street,
London EC1V
>> 4AD.
>>
>
>
>
> --
>
> --------------------------------------------------------------------
-------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative
Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt
>
>
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt
[[alternative HTML version deleted]]
Hi Andreia,
OK - I was able to reproduce this error with a toy example. I have a
fix for it, which I have committed it to the repository, and so it
should be fine in BayesPeak 1.4.1 and onwards.
Let me know if this solves the problem for you!
---
For the record, the problem is to do what I feel is a slightly
counter-intuitive behaviour of IRanges: In the subroutine
strand.split(), IRanges_JKA undergoes what is effectively:
bed <- IRanges_JKA
sel <- bed$strand == "+"
start(bed)[sel] ##error
When IRanges_JKA is constructed as in the code below, bed$strand comes
out as an Rle object instead of a factor. Therefore, sel is also an
Rle object, and it appears that you cannot subset with an Rle logical
object. I got round it by coercing it to a factor.
At first I wondered if this problem could be fixed by using a more
canonical accessor function:
bed <- IRanges_JKA
sel <- strand(bed) == "+"
start(bed)[sel] ##no error
Whereas bed$strand is an Rle object, strand(bed) is a normal factor,
and things can proceed.
Unfortunately, when bed$strand is not an Rle object, as in the package
examples, attempting to use this accessor function now returns a
"function does not exist" error, which is why I went with the coercion
approach. Is this behaviour intentional?
Thanks,
Jonathan
________________________________________
From: Andreia Fonseca [andreia.fonseca@gmail.com]
Sent: 20 July 2011 18:12
To: Jonathan Cairns
Cc: bioconductor
Subject: Re: error in bayespeak function
sorry, please disregard my last email. The RangedData is the object
IRanges_JKA_I and IRanges_JKA,
the error remains the same, it does not cahnge after attaching
rtracklayer
raw.output <- bayespeak(treatment=IRanges_JKA,
control=IRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
Error in `[.default`(space(bed), sel) : invalid subscript type 'S4'
after making
str(space(IRanges_JKA_I))
Factor w/ 25 levels "chr1","chr2",..: 1 1 1 1 1 1 1 1 1 1 ...
str(space(IRanges_JKA))
Factor w/ 25 levels "chr1","chr2",..: 1 1 1 1 1 1 1 1 1 1 ...
On Wed, Jul 20, 2011 at 6:06 PM, Andreia Fonseca <andreia.fonseca at="" gmail.com<mailto:andreia.fonseca="" at="" gmail.com="">> wrote:
Hi Jonathan,
after doing str(space(GIRanges_JKA)) and str(space(GIRanges_JKA_I))
it results in the following error:
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "space", for
signature "GRanges"
I have attached rtracklayer as you suggested and run the code again
and now the error meassage has changed, it seems is not being able to
find the strand information
raw.output <- bayespeak(treatment=GIRanges_JKA,
control=GIRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
Error in bed$strand : $ operator not defined for this S4 class
one other thing that I did was to use the example data that you
provide
sig <- read.table("H3K4me3-chr16.bed", skip=1,
colClasses=c("character", "numeric")[c(1,2,2,1,1,1,1,1,1)])
bgr <- read.table("Input-chr16.bed", colClasses=c("character",
"numeric")[c(1,2,2,1,1,1,1,1,1)])
sig <- RangedData(space=sig[,1], IRanges(start=sig[,2], end=sig[,3]),
strand=sig[,6])
bgr <- RangedData(space=bgr[,1], IRanges(start=bgr[,2], end=bgr[,3]),
strand=bgr[,6])> bgr <- read.table("Input-chr16.bed",
colClasses=c("character", "numeric")
and then I do not get an error when running bayespeak...
On Wed, Jul 20, 2011 at 5:49 PM, Jonathan Cairns <jonathan.cairns at="" cancer.org.uk<mailto:jonathan.cairns="" at="" cancer.org.uk="">> wrote:
Andreia,
That's very strange. What happens when you do:
str(space(GIRanges_JKA))
str(space(GIRanges_JKA_I))
Do either of these result in an error?
You could try attaching the package rtracklayer at the start; I find
that this sometimes fixes odd IRanges behaviour.
Jonathan
________________________________________
From: Andreia Fonseca
[andreia.fonseca@gmail.com<mailto:andreia.fonseca@gmail.com>]
Sent: 20 July 2011 17:11
To: Jonathan Cairns
Cc: bioconductor
Subject: Re: error in bayespeak function
Dear Jonathan,
Maybe it helps to see that my both sample and input information are
now effectively RangedData objects
IRanges_JKA
RangedData with 3850192 rows and 1 value column across 25 spaces
space ranges | strand
<factor> <iranges> | <rle>
1 chr1 [10071, 10120] | +
2 chr1 [10074, 10123] | +
3 chr1 [10075, 10124] | +
4 chr1 [10075, 10124] | -
5 chr1 [10106, 10155] | -
6 chr1 [10147, 10196] | -
7 chr1 [10148, 10197] | +
8 chr1 [10149, 10198] | +
9 chr1 [10150, 10199] | +
... ... ... ... ...
3850184 chrM [16491, 16540] | -
3850185 chrM [16496, 16545] | -
3850186 chrM [16499, 16548] | +
3850187 chrM [16502, 16551] | +
3850188 chrM [16506, 16555] | -
3850189 chrM [16507, 16556] | +
3850190 chrM [16515, 16564] | -
3850191 chrM [16516, 16565] | -
3850192 chrM [16521, 16570] | +
IRanges_JKA_I
RangedData with 6443227 rows and 1 value column across 25 spaces
space ranges | strand
<factor> <iranges> | <rle>
1 chr1 [10073, 10122] | -
2 chr1 [10165, 10214] | +
3 chr1 [10445, 10494] | +
4 chr1 [13064, 13113] | +
5 chr1 [16060, 16109] | +
6 chr1 [16416, 16465] | -
7 chr1 [20103, 20152] | +
8 chr1 [20103, 20152] | +
9 chr1 [51428, 51477] | -
... ... ... ... ...
6443219 chrM [16509, 16558] | +
6443220 chrM [16511, 16560] | -
6443221 chrM [16512, 16561] | +
6443222 chrM [16513, 16562] | -
6443223 chrM [16516, 16565] | +
6443224 chrM [16516, 16565] | -
6443225 chrM [16517, 16566] | +
6443226 chrM [16518, 16567] | -
6443227 chrM [16520, 16569] | -
On Wed, Jul 20, 2011 at 4:00 PM, Andreia Fonseca <andreia.fonseca at="" gmail.com<mailto:andreia.fonseca="" at="" gmail.com=""><mailto:andreia.fonseca at="" gmail.com<mailto:andreia.fonseca="" at="" gmail.com="">>> wrote:
Hi Jonathan,
thanks for the help, I have another error now! I have changed the code
as you suggested and I also spotted that in bayespeak I was calling
the bam object instead of the IRanges object, still the IRanges object
is not proper as you mentioned. I manage to create a RangeData object
but :
#call libraries
library(GenomicRanges)
library(BayesPeak)
library(ShortRead)
library(chipseq)
library(ChIPpeakAnno)
library(multicore)
library(GenomicFeatures)
#read sample JKA
JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique
_forfastq.fastq_SAM", overwrite=TRUE,destination="110402_SN365_B_s_2_s
eq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA<-readBamGappedAlignments(JKA)
GIRanges_JKA<-as(Granges_JKA, "GRanges")
IRanges_JKA<-as(GIRanges_JKA, "RangedData")
#read Input JKA
JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM", overwrite=TRUE,destination="110402_SN365_B_s_2
_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA_I<-readBamGappedAlignments(JKA_I)
GIRanges_JKA_I<-as(Granges_JKA_I, "GRanges")
IRanges_JKA_I<-as(GIRanges_JKA_I, "RangedData")
#Peak Calling with BayesPeak
raw.output <- bayespeak(treatment=IRanges_JKA,
control=IRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
error message
Error in `[.default`(space(bed), sel) : invalid subscript type 'S4'
any idea?
thanks
On Wed, Jul 20, 2011 at 3:38 PM, Jonathan Cairns <jonathan.cairns at="" cancer.org.uk<mailto:jonathan.cairns="" at="" cancer.org.uk=""><mailto:jonathan.cairns at="" cancer.org.uk<mailto:jonathan.cairns="" at="" cancer.org.uk="">>> wrote:
Hi Andreia,
On the line "IRanges_JKA<-ranges(Granges_JKA)", you are converting a
genomicRanges object to an IRanges object. BayesPeak accepts a
RangedData object, as opposed to an IRanges object (in order to retain
chromosome information). Replace
IRanges_JKA<-ranges(Granges_JKA)
with
IRanges_JKA<-as(Granges_JKA, "RangedData")
and it should run properly.
Hope this helps,
Jonathan
P.S. additionally, the line Library(BayesPeak) should be
library(BayesPeak) - you obviously know this, else you wouldn't be
getting the correct sessionInfo(), but I point this out in case
anybody else tries to run the code...
________________________________________
From: Andreia Fonseca [andreia.fonseca@gmail.com<mailto:andreia.fonsec a@gmail.com=""><mailto:andreia.fonseca@gmail.com<mailto:andreia.fonseca@g mail.com="">>]
Sent: 20 July 2011 15:24
To: Jonathan Cairns; bioconductor
Subject: error in bayespeak function
Dear all,
I am analyzing chipseq data and I am trying to use bayespeak package
for peak detection.
The code that I am using is
#call libraries
library(GenomicRanges)
Library(BayesPeak)
library(ShortRead)
library(chipseq)
library(ChIPpeakAnno)
library(multicore)
library(GenomicFeatures)
#read sample JKA
JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique
_forfastq.fastq_SAM", overwrite=TRUE,destination="110402_SN365_B_s_2_s
eq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA<-readBamGappedAlignments(JKA)
IRanges_JKA<-ranges(Granges_JKA)
#read Input JKA
JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_uniq
ue_forfastq.fastq_SAM", overwrite=TRUE,destination="110402_SN365_B_s_2
_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
Granges_JKA_I<-readBamGappedAlignments(JKA_I)
IRanges_JKA_I<-ranges(Granges_JKA_I)
#Peak Calling with BayesPeak
raw.output <- bayespeak(treatment=JKA, control=JKA_I,use.multicore =
TRUE, mc.cores = 4)
after the last command I am getting the forllowing error:
Error in substring(temp[1], 1, 5) : invalid multibyte string at '<ed>'
I also tried to remove the use of parallelization but the error
remains the same, can someone tell me what I am doing wrong ?
thanks for the help,
Andreia
bellow is the information concerning sessionInfo
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BayesPeak_1.4.0 GenomicFeatures_1.4.3
[3] multicore_0.1-5 ChIPpeakAnno_1.8.0
[5] limma_3.8.2 org.Hs.eg.db_2.5.0
[7] GO.db_2.4.1 RSQLite_0.9-1
[9] DBI_0.2-5 AnnotationDbi_1.14.1
[11] BSgenome.Ecoli.NCBI.20080805_1.3.17 multtest_2.8.0
[13] Biobase_2.12.2 biomaRt_2.8.1
[15] chipseq_1.2.0 BSgenome_1.20.0
[17] ShortRead_1.10.4 Rsamtools_1.4.2
[19] lattice_0.19-30 Biostrings_2.20.1
[21] GenomicRanges_1.4.6 IRanges_1.10.4
loaded via a namespace (and not attached):
[1] grid_2.13.1 hwriter_1.2 MASS_7.3-13
RCurl_1.4-2
[5] rtracklayer_1.12.4 splines_2.13.1 survival_2.36-9
tools_2.13.1
[9] XML_3.1-0
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral at fm.ul.pt<mailto:email%3aandreiaamaral at="" fm.ul.pt=""><mailto:email%3aandreiaamaral at="" fm.ul.pt<mailto:email%253aandreiaamaral="" at="" fm.ul.pt="">><mailto:email%3aandreiaamaral at="" fm.ul.pt<mailto:email%253aandreiaamaral="" at="" fm.ul.pt=""><mailto:email%253aandreiaamaral at="" fm.ul.pt<mailto:email%25253aandreiaamaral="" at="" fm.ul.pt="">>> ;
andreiaamaral at fc.ul.pt<mailto:andreiaamaral at="" fc.ul.pt=""><mailto:andreiaamaral at="" fc.ul.pt<mailto:andreiaamaral="" at="" fc.ul.pt="">><mailto:andreiaamaral at="" fc.ul.pt<mailto:andreiaamaral="" at="" fc.ul.pt=""><mailto:andreiaamaral at="" fc.ul.pt<mailto:andreiaamaral="" at="" fc.ul.pt="">>>
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--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral at fm.ul.pt<mailto:email%3aandreiaamaral at="" fm.ul.pt=""><mailto:email%3aandreiaamaral at="" fm.ul.pt<mailto:email%253aandreiaamaral="" at="" fm.ul.pt="">> ; andreiaamaral
at fc.ul.pt<mailto:andreiaamaral at="" fc.ul.pt=""><mailto:andreiaamaral at="" fc.ul.pt<mailto:andreiaamaral="" at="" fc.ul.pt="">>
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral at fm.ul.pt<mailto:email%3aandreiaamaral at="" fm.ul.pt=""><mailto:email%3aandreiaamaral at="" fm.ul.pt<mailto:email%253aandreiaamaral="" at="" fm.ul.pt="">> ; andreiaamaral
at fc.ul.pt<mailto:andreiaamaral at="" fc.ul.pt=""><mailto:andreiaamaral at="" fc.ul.pt<mailto:andreiaamaral="" at="" fc.ul.pt="">>
NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for the above-
named person(s). If you are not the intended recipient, notify the
sender immediately, delete this email from your system and do not
disclose or use for any purpose.
We may monitor all incoming and outgoing emails in line with current
legislation. We have taken steps to ensure that this email and
attachments are free from any virus, but it remains your
responsibility to ensure that viruses do not adversely affect you.
Cancer Research UK
Registered in England and Wales
Company Registered Number: 4325234.
Registered Charity Number: 1089464 and Scotland SC041666
Registered Office Address: Angel Building, 407 St John Street, London
EC1V 4AD.
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral at fm.ul.pt<mailto:email%3aandreiaamaral at="" fm.ul.pt=""> ; andreiaamaral at fc.ul.pt<mailto:andreiaamaral at="" fc.ul.pt="">
--
----------------------------------------------------------------------
-----------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral at fm.ul.pt<mailto:email%3aandreiaamaral at="" fm.ul.pt=""> ; andreiaamaral at fc.ul.pt<mailto:andreiaamaral at="" fc.ul.pt="">
NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for the above-
named person(s). If you are not the intended recipient, notify the
sender immediately, delete this email from your system and do not
disclose or use for any purpose.
We may monitor all incoming and outgoing emails in line with current
legislation. We have taken steps to ensure that this email and
attachments are free from any virus, but it remains your
responsibility to ensure that viruses do not adversely affect you.
Cancer Research UK
Registered in England and Wales
Company Registered Number: 4325234.
Registered Charity Number: 1089464 and Scotland SC041666
Registered Office Address: Angel Building, 407 St John Street, London
EC1V 4AD.