Hi bioconductor group,

I'm working on a chIPseq dataset and trying to annotated my peaks.  So, after getting the gene symbol using biomart and want to merge it back to my bed file and it give me this error.  Any help is appreciated.  Thanks. QT


    bed_file_orig <- read.delim(file_name, header=FALSE, skip=1)
            bed_file <- bed_file_orig[!(stri_sub(bed_file_orig$V1, 1, 2)%in%c("HG", "MT", "GL")),]
            peakList <- BED2RangedData(bed_file)
            annotatedPeak = annotatePeakInBatch(peakList, AnnotationData=hs_annotation_tss)

            #add gene ids to the peak: using addGeneIDs gives error if the database does not contain the feature.  So use biomart
            #annotatedPeak_tss <- addGeneIDs(annotatedPeak_tss,"org.Hs.eg.db",c("symbol", "genename"))
            feature_ids <- unique(annotatedPeak$feature)
            feature_ids<-feature_ids[!is.na(feature_ids)]
            feature_ids<-feature_ids[feature_ids!=""]
            IDs2Add<-getBM(attributes=c("ensembl_gene_id","external_gene_id"),filters = "ensembl_gene_id", values = feature_ids, mart=mart)

            out_file_name <- paste("../data/processed/",patient,"_",TF,"_",cond_out, ".csv", sep="")
            write.csv(annotatedPeak, file=out_file_name)
            annotatedPeak <- read.csv(out_file_name)
            annotatedPeak_reorder <- annotatedPeak[,c(9, 1:8, 10:15)]
            annotatedPeak_tss <- merge(annotatedPeak_reorder, IDs2Add, by.x="feature", b.y="ensembl_gene_id")


Error in merge.data.frame(annotatedPeak_reorder, IDs2Add, by.x = "feature",  :
  'by.x' and 'by.y' specify different numbers of columns
_______________________________
Nhu Quynh T. Tran, Ph.D.
Assistant Professor of Preventive Medicine
University of Tennessee Health Science Center
66 N. Pauline, Suite 633
Memphis, TN 38105
Phone: 901-448-1361
Fax: 901-448-7041
Email: qtran1@uthsc.edu<mailto:qtran1@uthsc.edu>



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