ChIPpeakAnno Biomart Archive annotation querying
0
0
Entering edit mode
@khademul-islam-3826
Last seen 5.9 years ago
Hi, This way it works perfectly !!! many thanks again Khademul ===================================================== On Mon, Nov 30, 2009 at 3:56 PM, Julie Zhu <julie.zhu@umassmed.edu> wrote: > Hi Khademul, > > I think querying bioMart archive data failed, could you please try to get > annotation using this method before calling annotatePeakInBatch? Thanks! > Annotation = getAnnotation(mart, featureType="TSS") > annotatedPeak = annotatePeakInBatch(myPeak, AnnotationData= Annotation) > > > Best regards, > > Julie > > > > ******************************************* > Julie Zhu, Ph.D > Research Associate Professor > Program Gene Function and Expression > University of Massachusetts Medical School > 364 Plantation Street, Room 613 > Worcester, MA 01605 > 508-856-5256 > http://www.umassmed.edu/pgfe/faculty/zhu.cfm > > > > > On 11/30/09 7:13 AM, "Khademul Islam" <khademul.islam@gmail.com> wrote: > > > 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=spa ce) > data(TSS.human.NCBI36) > annotatedPeak = annotatePeakInBatch(myPeak, > AnnotationData=TSS.human.NCBI36) > result <- as.data.frame(annotatedPeak) > > > *However, 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_positi on","end_position","strand"), > mart=mart) > > ]] > > > *#### So, could you please tell me how to solve this problem ??? > * > Thank you > > khademul > > [[alternative HTML version deleted]]
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt • 873 views
ADD COMMENT

Login before adding your answer.

Traffic: 287 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6