Question: bug in dba.overlap (dba.plotVenn)
0
gravatar for jeremydt
2.2 years ago by
jeremydt0
San Diego
jeremydt0 wrote:

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 • 440 views
ADD COMMENTlink modified 2.2 years ago by Rory Stark2.8k • written 2.2 years ago by jeremydt0
Answer: bug in dba.overlap (dba.plotVenn)
0
gravatar for Rory Stark
2.2 years ago by
Rory Stark2.8k
CRUK, Cambridge, UK
Rory Stark2.8k wrote:

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

ADD COMMENTlink written 2.2 years ago by Rory Stark2.8k
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