 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

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