ChIPpeakAnno Biomart annotation
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@khademul-islam-3826
Last seen 5.2 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 [[alternative HTML version deleted]]
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt • 1.1k views
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 10 days ago
United States
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_p > osition","strand"), mart=mart) > > ]] > > > #### So, could you please tell me how to solve this problem ??? > > Thank you > > khademul > [[alternative HTML version deleted]]
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