Entering edit mode
Hi Matt-
Yep, it's a bug!
If you plot this as a Venn, you can see one peakset has zero elements:
> dba.plotVenn(chip, 16:19)
There's no check when this is converted to a GRanges object. I'll fix
this
and check it in soon. In the mean time, you can work around this by
using
data frames instead of GRanges, either by:
> chip.OL = dba.overlap(chip,
>c(16,17,18,19),mode=DBA_OLAP_PEAKS,DataType=DBA_DATA_FRAME)
or by changing the default data type:
> chip$config$DataType = DBA_DATA_FRAME
I tend to run with DBA_DATA_FRAME as the default, which is probably
why I
didn't spot this bug before.
Cheers-
Rory
On 14/11/2013 16:00, "Matt Zinkgraf" <mzinkgraf at="" gmail.com=""> wrote:
>Hi Roy
>Thanks for the response. The chip object can be found at
>https://dl.dropboxusercontent.com/u/96655685/chip.rdata
>
>Matt
>
>-----Original Message-----
>From: Rory Stark [mailto:Rory.Stark at cruk.cam.ac.uk]
>Sent: Thursday, November 14, 2013 4:05 AM
>To: mzinkgraf at gmail.com
>Cc: bioconductor at r-project.org
>Subject: Re: DiffBind and GRanges error extracting overlapping peaks
>using dba.overlap
>
>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.
>
>
