[BioC] DiffBind and GRanges error extracting overlapping peaks using dba.overlap
Matt Zinkgraf [guest]
guest at bioconductor.org
Thu Nov 14 02:04:33 CET 2013
Hello
I am using DiffBind to identify consensus binding sites for multiple transcription factors that have biological replicates. In addition, I want to investigate the overlap of binding sites across the transcription factors. I am able to call consensus peaks for each transcription factor and calculate the overlap rate and plot overlaps with dba.plotVenn but I am getting an error from GRanges when trying to extract the actual overlapping peaks using dba.overlap and DBA_OLAP_PEAKS. Any suggestions on why I am getting this error?
Thanks
Matt
> #load datasets
> chip= dba(sampleSheet="chip_datasets_testing.csv", peakCaller="bed")
a4142.1 a21 ARK2 1 bed
a4142.2 a22 ARK2 2 bed
a0304.1 a23 ARK2 1 bed
a0304.2 a24 ARK2 2 bed
r4748.1 r11 REV 1 bed
r8586.1 r21 REV 1 bed
r8586.2 r22 REV 2 bed
c4344.1 c11 PCN 1 bed
c4344.2 c12 PCN 2 bed
c4546.1 c21 PCN 1 bed
c4546.2 c22 PCN 2 bed
a3738.1 a11 ARK1 1 bed
a3738.2 a12 ARK1 2 bed
a3940.2 a14 ARK1 2 bed
a3940.1 a13 ARK1 1 bed
>
> #create consensus peaks and plot overlap
> chip = dba.peakset(chip, consensus = DBA_TREATMENT, minOverlap = 0.5)
Add consensus: ARK2
Add consensus: REV
Add consensus: PCN
Add consensus: ARK1
>
> chip
19 Samples, 12123 sites in matrix (29678 total):
ID Condition Treatment Replicate Peak.caller Intervals
1 a4142.1 a21 ARK2 1 bed 3239
2 a4142.2 a22 ARK2 2 bed 2026
3 a0304.1 a23 ARK2 1 bed 2718
4 a0304.2 a24 ARK2 2 bed 581
5 r4748.1 r11 REV 1 bed 6958
6 r8586.1 r21 REV 1 bed 595
7 r8586.2 r22 REV 2 bed 869
8 c4344.1 c11 PCN 1 bed 8526
9 c4344.2 c12 PCN 2 bed 803
10 c4546.1 c21 PCN 1 bed 5524
11 c4546.2 c22 PCN 2 bed 5320
12 a3738.1 a11 ARK1 1 bed 7443
13 a3738.2 a12 ARK1 2 bed 7004
14 a3940.2 a14 ARK1 2 bed 5697
15 a3940.1 a13 ARK1 1 bed 761
16 ARK2 a21-a22-a23-a24 ARK2 1-2 bed 2030
17 REV r11-r21-r22 REV 1-2 bed 548
18 PCN c11-c12-c21-c22 PCN 1-2 bed 3500
19 ARK1 a11-a12-a14-a13 ARK1 1-2 bed 6210
>
> dba.overlap(chip,c(16,17,18,19), mode=DBA_OLAP_RATE)
[1] 10006 1733 327 11
>
> chip.OL = dba.overlap(chip, c(16,17,18,19),mode=DBA_OLAP_PEAKS)
Error in validObject(.Object) :
invalid class âGRangesâ object: NROW(strand(x)) != length(x)
-- output of sessionInfo():
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] DiffBind_1.8.2 Biobase_2.22.0 GenomicRanges_1.14.3
[4] XVector_0.2.0 IRanges_1.20.5 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] amap_0.8-7 bitops_1.0-6 caTools_1.16
[4] edgeR_3.4.0 gdata_2.13.2 gplots_2.12.1
[7] gtools_3.1.1 KernSmooth_2.23-10 limma_3.18.2
[10] RColorBrewer_1.0-5 stats4_3.0.2 tools_3.0.2
[13] zlibbioc_1.8.0
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