Entering edit mode
Khademul Islam
▴
30
@khademul-islam-3826
Last seen 7.7 years ago
Hi,
The ChIPpeakAnno is working fine with R 2.10.0 with annotation from
TSS.NCBI36..............like following:
library(ChIPpeakAnno)
myPeak=RangedData(IRanges(start=start,end=end,names=names),space=space
)
data(TSS.human.NCBI36)
annotatedPeak = annotatePeakInBatch(myPeak,
AnnotationData=TSS.human.NCBI36)
result <- as.data.frame(annotatedPeak)
*H**owever, if I want to get annotation from Biomart (in stead of
TSS.human.NCBI36) archive version 51, I am getting following error:*
> mart <- useMart(biomart="ensembl_mart_51",
dataset="hsapiens_gene_ensembl", archive=TRUE)
Checking attributes ... ok
Checking filters ... ok
> annotatedPeak = annotatePeakInBatch(myPeak, mart, featureType="TSS")
##
or, annotatedPeak = annotatePeakInBatch(myPeak, mart=mart,
featureType="TSS")
No AnnotationData as RangedData is passed in, so now querying biomart
database for AnnotationData!
*Error in annotatePeakInBatch(myPeak, mart, featureType = "TSS") : *
* element 1 is empty;*
* the part of the args list of 'class' being evaluated was:*
* (AnnotationData)*
>
> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-apple-darwin9.8.0
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPpeakAnno_1.2.0 org.Hs.eg.db_2.3.6
[3] GO.db_2.3.5 RSQLite_0.7-3
[5] DBI_0.2-4 AnnotationDbi_1.8.1
[7] BSgenome.Ecoli.NCBI.20080805_1.3.15 BSgenome_1.14.2
[9] Biostrings_2.14.8 IRanges_1.4.9
[11] multtest_2.2.0 Biobase_2.6.0
[13] biomaRt_2.2.0
loaded via a namespace (and not attached):
[1] MASS_7.3-4 RCurl_1.2-1 XML_2.6-0 splines_2.10.0
[5] survival_2.35-7 tools_2.10.0
[[ I can get annotation data from biomart (similar as "getAnnotation"
function does) without any problem.....
mart <- useMart(biomart="ensembl_mart_51",
dataset="hsapiens_gene_ensembl",
archive=TRUE)
biomart_data =
getBM(attributes=c("ensembl_gene_id","chromosome_name","start_position
","end_position","strand"),
mart=mart)
]]
*#### So, could you please tell me how to solve this problem ???*
Thank you
khademul
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