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
