Hi, I recently made venn diagrams from chip-seq data using the Chippeakanno library and I was wondering how to get the intersect of these venn diagrams and annotate them (closest gene, within intron/exon, distance from TSS) Thanks, Ying Wu m1 = read.table("./methyl1_peaks.bed", sep="\t") m2 = read.table("./methyl2_peaks.bed", sep="\t") m3 = read.table("./methyl3_peaks.bed", sep="\t") m4 = read.table("./methyl4_peaks.bed", sep="\t") m1.r = BED2RangedData(m1) m2.r = BED2RangedData(m2) m3.r = BED2RangedData(m3) m4.r = BED2RangedData(m4) mkd = makeVennDiagram(RangedDataList(m1.r,m2.r,m3.r,m4.r), NameOfPeaks=c("M1", "M2", "M3", "M4"), totalTest=200000) > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ChIPpeakAnno_1.9.5 gplots_2.8.0 [3] caTools_1.12 bitops_1.0-4.1 [5] gdata_2.8.2 gtools_2.6.2 [7] limma_3.8.2 org.Hs.eg.db_2.5.0 [9] GO.db_2.5.0 RSQLite_0.9-4 [11] DBI_0.2-5 AnnotationDbi_1.14.1 [13] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.20.0 [15] GenomicRanges_1.4.6 Biostrings_2.20.1 [17] IRanges_1.10.4 multtest_2.8.0 [19] Biobase_2.12.2 biomaRt_2.8.1 loaded via a namespace (and not attached): [1] MASS_7.3-13 RCurl_1.6-6 splines_2.13.0 survival_2.36-9 [5] tools_2.13.0 XML_3.4-0 [[alternative HTML version deleted]]

Ying, You could run findOverlappingPeaks function followed by annotatePeakInBatch. Here is an example for getting annotated intersection between m1.r and m2.r. m1m2.ann = annotatePeakInBatch(findOverlappingPeaks(m1.r, m2.r, multiple=FALSE, maxgap=0, NameOfPeaks1 = "m1", NameOfPeaks2 = "m2")$mergedPeaks, Annotation=yourAnnotationData) Here is an example for getting annotated intersection between m1.r, m2.r and m3.r. m1m2m3.ann = annotatePeakInBatch(findOverlappingPeaks( findOverlappingPeaks(m1.r, m2.r, multiple=FALSE, maxgap=0, NameOfPeaks1 = "m1", NameOfPeaks2 = "m2")$mergedPeaks, m3.r, multiple=FALSE, maxgap=0, NameOfPeaks1="m1m2", NameOfPeaks2="m3")$mergedPeaks, Annotation=yourAnnotationData) Best regards, Julie On 7/27/11 4:01 PM, "Ying W" <daiyingw at="" gmail.com=""> wrote: > Hi, > I recently made venn diagrams from chip-seq data using the Chippeakanno > library and I was wondering how to get the intersect of these venn diagrams > and annotate them (closest gene, within intron/exon, distance from TSS) > > Thanks, > Ying Wu > > m1 = read.table("./methyl1_peaks.bed", sep="\t") > m2 = read.table("./methyl2_peaks.bed", sep="\t") > m3 = read.table("./methyl3_peaks.bed", sep="\t") > m4 = read.table("./methyl4_peaks.bed", sep="\t") > > m1.r = BED2RangedData(m1) > m2.r = BED2RangedData(m2) > m3.r = BED2RangedData(m3) > m4.r = BED2RangedData(m4) > mkd = makeVennDiagram(RangedDataList(m1.r,m2.r,m3.r,m4.r), > NameOfPeaks=c("M1", "M2", "M3", "M4"), totalTest=200000) > >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] ChIPpeakAnno_1.9.5 gplots_2.8.0 > [3] caTools_1.12 bitops_1.0-4.1 > [5] gdata_2.8.2 gtools_2.6.2 > [7] limma_3.8.2 org.Hs.eg.db_2.5.0 > [9] GO.db_2.5.0 RSQLite_0.9-4 > [11] DBI_0.2-5 AnnotationDbi_1.14.1 > [13] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.20.0 > [15] GenomicRanges_1.4.6 Biostrings_2.20.1 > [17] IRanges_1.10.4 multtest_2.8.0 > [19] Biobase_2.12.2 biomaRt_2.8.1 > > loaded via a namespace (and not attached): > [1] MASS_7.3-13 RCurl_1.6-6 splines_2.13.0 survival_2.36-9 > [5] tools_2.13.0 XML_3.4-0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >