bug in dba.overlap (dba.plotVenn)
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Entering edit mode
jeremydt • 0
@jeremydt-13101
Last seen 6.9 years ago
San Diego

To DiffBind users & developers,

We have found a bug in dba.overlap introduced after Bioconductor 3.2, and are posting the workaround here as well.

When using dba.plotVenn (which calls dba.overlap) on consensus peaks, in certain circumstances some of the information is not built out correctly.

data(tamoxifen_peaks)

tamoxifen2 = dba.peakset(tamoxifen, consensus = DBA_TISSUE, minOverlap=0.01) # Vignette has minOverlap=0.66

dba.plotVenn(tamoxifen2, tamoxifen2$masks$Consensus)

 Error in pv$called[, A] : subscript out of bounds

WORKAROUND:

tamoxifen3 <- dba(tamoxifen2, mask=tamoxifen2$masks$Consensus, minOverlap=1)

dba.plotVenn(tamoxifen3, tamoxifen3$masks$Consensus)

 

ACTUAL BUG:

In the Vignette, the default params result 'if (pv$totalMerged != nrow(pv$binding))' evaluating to true, and a call to pv.vectors which rectifies this issue.

 

 


sessionInfo()

sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.12.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] DiffBind_2.4.2             SummarizedExperiment_1.6.1
 [3] DelayedArray_0.2.4         matrixStats_0.52.2        
 [5] Biobase_2.36.2             GenomicRanges_1.28.2      
 [7] GenomeInfoDb_1.12.0        IRanges_2.10.1            
 [9] S4Vectors_0.14.1           BiocGenerics_0.22.0       
[11] BiocInstaller_1.26.0      

loaded via a namespace (and not attached):
 [1] edgeR_3.18.1             splines_3.4.0            gtools_3.5.0            
 [4] assertthat_0.2.0         latticeExtra_0.6-28      amap_0.8-14             
 [7] RBGL_1.52.0              GenomeInfoDbData_0.99.0  Rsamtools_1.28.0        
[10] ggrepel_0.6.5            Category_2.42.0          RSQLite_1.1-2           
[13] backports_1.1.0          lattice_0.20-35          limma_3.32.2            
[16] digest_0.6.12            RColorBrewer_1.1-2       XVector_0.16.0          
[19] checkmate_1.8.2          colorspace_1.3-2         Matrix_1.2-10           
[22] plyr_1.8.4               GSEABase_1.38.0          XML_3.98-1.7            
[25] pheatmap_1.0.8           ShortRead_1.34.0         biomaRt_2.32.0          
[28] genefilter_1.58.1        zlibbioc_1.22.0          xtable_1.8-2            
[31] GO.db_3.4.1              scales_0.4.1             brew_1.0-6              
[34] gdata_2.17.0             BiocParallel_1.10.1      tibble_1.3.1            
[37] annotate_1.54.0          ggplot2_2.2.1            GenomicFeatures_1.28.0  
[40] lazyeval_0.2.0           survival_2.41-3          magrittr_1.5            
[43] memoise_1.1.0            systemPipeR_1.10.0       fail_1.3                
[46] gplots_3.0.1             hwriter_1.3.2            GOstats_2.42.0          
[49] graph_1.54.0             tools_3.4.0              BBmisc_1.11             
[52] stringr_1.2.0            sendmailR_1.2-1          munsell_0.4.3           
[55] locfit_1.5-9.1           AnnotationDbi_1.38.0     Biostrings_2.44.0       
[58] compiler_3.4.0           caTools_1.17.1           rlang_0.1.1             
[61] grid_3.4.0               RCurl_1.95-4.8           rjson_0.2.15            
[64] AnnotationForge_1.18.0   bitops_1.0-6             base64enc_0.1-3         
[67] gtable_0.2.0             DBI_0.6-1                R6_2.2.1                
[70] GenomicAlignments_1.12.1 dplyr_0.5.0              rtracklayer_1.36.2      
[73] KernSmooth_2.23-15       stringi_1.1.5            BatchJobs_1.6           
[76] Rcpp_0.12.11 

DiffBind bugs • 1.2k views
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0
Entering edit mode
Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 2 days ago
Cambridge, UK

Yup, this is a bug. Thanks for the clear bug report and simple reproduction case.

I have checked in a fix, it will appear in DiffBind_2.4.3 soon.

-Rory

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