Hi everybody,

I need help now, I have two files where are recorded peaks from Chip-seq experiment :

WT <- import.bed('L18_19_peaks.TSS_mRNA.IntergenicClean.bed')
ts140 <- import.bed('L18_20_peaks.TSS_mRNA.IntergenicClean.bed')

WT
> `GRanges object with 313 ranges and 2 metadata columns:
    seqnames        ranges strand |                   name     score
       <Rle>     <IRanges>  <Rle> |            <character> <numeric>
[1]     chrI   68139-69297      - |    L18_19.macs2_peak_7   7.32153
[2]     chrI 141525-143590      - |   L18_19.macs2_peak_12  15.14930
[3]    chrII 137881-140936      - |   L18_19.macs2_peak_38  13.39680
[4]    chrII 165003-165559      - |   L18_19.macs2_peak_42   8.33408
[5]    chrII 217140-217379      - |   L18_19.macs2_peak_46   3.81654
...      ...           ...    ... .                    ...       ...
[309]   chrXVI 789657-789860      + | L18_19.macs2_peak_1494   3.85548
[310]   chrXVI 812791-813769      - | L18_19.macs2_peak_1498   5.25748
[311]   chrXVI 828737-829519      + | L18_19.macs2_peak_1501   4.59543
[312]   chrXVI 927613-928569      - | L18_19.macs2_peak_1521   5.68587
[313]   chrXVI 930484-930724      + | L18_19.macs2_peak_1522   3.38815
  -------
  seqinfo: 16 sequences from an unspecified genome; no seqlengths

I am trying to create a Venn diagram with Vennerable package just like this :

ovl <- subsetByOverlaps(WT, ts140)
WT_uniq <- GenomicRanges::setdiff(WT, ts140)
ts140_uniq <- GenomicRanges::setdiff(ts140, WT)

venn <- Venn(SetNames=c("WT", "ts140"), 
             Weight=c(
               '10'=length(WT_uniq), 
               '11'=length(ovl), 
               '01'=length(ts140_uniq)

             )
)
plot(venn)

The result is :

However, length(WT) is 313, meaning there are 313 peaks, so the numbers on the Venn diagram do not represent peaks numbers, since 247+261!=313. How could I get the Venn diagram with the nb of peaks please ?

Yours :)