[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 “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    

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