Entering edit mode
José LÓPEZ
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110
@jose-lopez-5444
Last seen 5.4 years ago
Dear Julie,
I am using findOverlappingPeaks and makeVennDiagram to compare 2 set
of peaks (A and B).
I get overlapping peaks of A with B ($Peaks1withOverlaps) (9992 see
below). My question is to how can I get those peaks specific to A
(13268) and those specific to B (2640)?
I also tried with subsetByOverlaps from (GenomicRanges package) and
get the intersect between A and B (9992 as with ChiPpeakAnno
functions). Then, to identify peaks that do not overlap tried to
isolate those A regions that were not present in the overlap with B,
but get an error (see below)...
> noOlap = peaks_AcH3_Ranged[!peaks_A_Ranged %in% peaks_B_Ranged]
Error in peaks_AcH3_Ranged[!peaks_A_Ranged %in% peaks_B_Ranged] :
selecting spaces: invalid subscript type
Thank you in advance for your suggestions,
Jose
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#load ChiPpeakAnno
> library (ChIPpeakAnno)
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: gdata
The following object(s) are masked from package:stats:
nobs
The following object(s) are masked from package:utils:
object.size
Loading required package: caTools
Loading required package: bitops
Loading required package: grid
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: MASS
Attaching package: gplots
The following object(s) are masked from package:stats:
lowess
Loading required package: BiocGenerics
Attaching package: BiocGenerics
The following object(s) are masked from package:gdata:
combine
The following object(s) are masked from package:stats:
xtabs
The following object(s) are masked from package:base:
anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
get, intersect, lapply, Map, mapply,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position,
rbind, Reduce, rep.int, rownames, sapply,
setdiff, table, tapply, union, unique
Loading required package: biomaRt
Loading required package: multtest
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: multtest
The following object(s) are masked from package:gplots:
wapply
Loading required package: IRanges
Attaching package: IRanges
The following object(s) are masked from package:gplots:
space
The following object(s) are masked from package:caTools:
runmean
The following object(s) are masked from package:gdata:
trim
Loading required package: Biostrings
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: BSgenome.Ecoli.NCBI.20080805
Loading required package: GO.db
Loading required package: AnnotationDbi
Attaching package: AnnotationDbi
The following object(s) are masked from package:MASS:
select
Loading required package: DBI
Loading required package: org.Hs.eg.db
Loading required package: limma
Warning messages:
1: package gtools was built under R version 2.15.1
2: package gdata was built under R version 2.15.1
3: package KernSmooth was built under R version 2.15.1
4: package MASS was built under R version 2.15.1
5: package IRanges was built under R version 2.15.1
6: package GenomicRanges was built under R version 2.15.1
7: replacing previous import space when loading IRanges
#Generate GRanges objects
> peaks_A = read.table("data_A.txt")
> dim(peaks_A)
[1] 23260 16
> peaks_A_Ranged = BED2RangedData(peaks_A,header=F)
> peaks_A_Ranged
RangedData with 23260 rows and 2 value columns across 21 spaces
space ranges | strand score
<factor> <iranges> | <numeric> <numeric>
00001 1 [3658000, 3663999] | 1 1
00002 1 [4481600, 4483799] | 1 1
00003 1 [4486200, 4488199] | 1 1
00004 1 [4561200, 4562399] | 1 1
00005 1 [4774000, 4776599] | 1 1
00006 1 [4796800, 4799399] | 1 1
00007 1 [4846400, 4849799] | 1 1
00008 1 [5007000, 5013799] | 1 1
00009 1 [5072800, 5075999] | 1 1
... ... ... ... ... ...
23252 X [165110000, 165112999] | 1 1
23253 X [165474200, 165475399] | 1 1
23254 X [165755800, 165759199] | 1 1
23255 X [166317200, 166320199] | 1 1
23256 X [166416000, 166421999] | 1 1
23257 Y [ 234000, 234799] | 1 1
23258 Y [ 346400, 347799] | 1 1
23259 Y [ 581200, 582799] | 1 1
23260 Y [ 621400, 623599] | 1 1
> peaks_B = read.table("data_B.txt")
> dim(peaks_B)
[1] 12632 16
> peaks_B_Ranged = BED2RangedData(peaks_B,header=F)
> peaks_B_Ranged
RangedData with 12632 rows and 2 value columns across 20 spaces
space ranges | strand score
<factor> <iranges> | <numeric> <numeric>
00001 1 [3660400, 3662799] | 1 1
00002 1 [4775200, 4777199] | 1 1
00003 1 [4797000, 4798399] | 1 1
00004 1 [6204200, 6205799] | 1 1
00005 1 [7076400, 7080599] | 1 1
00006 1 [9288400, 9290999] | 1 1
00007 1 [9538200, 9541999] | 1 1
00008 1 [9764400, 9766399] | 1 1
00009 1 [9998600, 9999999] | 1 1
... ... ... ... ... ...
12624 X [149932200, 149934799] | 1 1
12625 X [151695800, 151697199] | 1 1
12626 X [152057200, 152059599] | 1 1
12627 X [154255600, 154257999] | 1 1
12628 X [159173200, 159175599] | 1 1
12629 X [160707200, 160709599] | 1 1
12630 X [162676400, 162677599] | 1 1
12631 X [166356400, 166384999] | 1 1
12632 X [166416000, 166421999] | 1 1
#find overlaps A,B.
> t1 = findOverlappingPeaks (peaks_A_Ranged, peaks_B_Ranged, maxgap =
0, NameOfPeaks1 = "A", NameOfPeaks2 = "B", select = "all")
There were 20 warnings (use warnings() to see them)
> overlappingPeaks = as.data.frame(t1$Peaks1withOverlaps)
> head(overlappingPeaks)
space start end width names strand
1 1 3658000 3663999 6000 00001 +
2 1 4774000 4776599 2600 00005 +
3 1 4796800 4799399 2600 00006 +
4 1 6202800 6207199 4400 00010 +
5 1 7076200 7081599 5400 00014 +
6 1 9285400 9290999 5600 00017 +
> dim(overlappingPeaks)
[1] 9992 6
> write.table(as.data.frame(t1$Peaks1withOverlaps),
file="overlappingPeaks.txt", sep="\t", row.names=F)
#perform venn diagram
> makeVennDiagram(RangedDataList(peaks_A_Ranged, peaks_B_Ranged),
NameOfPeaks=c("A","B"), maxgap = 0, totalTest = 3E4, cex =1,
counts.col='red', useFeature=F)
$p.value
[1] 1.455914e-08
$vennCounts
A B Counts
[1,] 0 0 4100
[2,] 0 1 2640
[3,] 1 0 13268
[4,] 1 1 9992
attr(,"class")
[1] "VennCounts"
Warning message:
In findOverlappingPeaks(Peaks[[1]], Peaks[[2]], NameOfPeaks1 =
NameOfPeaks[1], :
Please use select instead of multiple!
> dev.copy2eps(file='VennDiagram.eps')
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets
methods base
other attached packages:
[1] ChIPpeakAnno_2.4.0
limma_3.12.1 org.Hs.eg.db_2.7.1
[4] GO.db_2.7.1
RSQLite_0.11.1 DBI_0.2-5
[7] AnnotationDbi_1.18.1 BSgenome.Ecoli.NCBI.
20080805_1.3.17 BSgenome_1.24.0
[10] GenomicRanges_1.8.9
Biostrings_2.24.1 IRanges_1.14.4
[13] multtest_2.12.0
Biobase_2.16.0 biomaRt_2.12.0
[16] BiocGenerics_0.2.0
gplots_2.11.0 MASS_7.3-19
[19] KernSmooth_2.23-8
caTools_1.13 bitops_1.0-4.1
[22] gdata_2.11.0 gtools_2.7.0
loaded via a namespace (and not attached):
[1] RCurl_1.91-1 splines_2.15.0 stats4_2.15.0
survival_2.36-14 XML_3.9-4
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