[BioC] DiffBind and GRanges error extracting overlapping peaks using dba.overlap
Rory Stark
Rory.Stark at cruk.cam.ac.uk
Thu Nov 14 13:04:58 CET 2013
Hi Matt-
Your code looks good -- this looks like a bug. It must be something about
the specific 4-way overlap that you are doing as I can't reproduce it with
some datasets I have.
Is there a way you can share the DiffBind Object ("chip") with me so I can
debug it? Dropbox perhaps?
Cheers-
Rory
On 14/11/2013 01:04, "Matt Zinkgraf [guest]" <guest at bioconductor.org>
wrote:
>
>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
>
>--
>Sent via the guest posting facility at bioconductor.org.
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