[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 “GRanges” 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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