DiffBind: Error in if (res$config$bCorPlot) { : the condition has length > 1
Entering edit mode
Last seen 16 months ago
United States

I'm getting an error repeatable error when I try to run code that worked with previous versions of DiffBind (3.4.11)

meta <- read_csv("../01b_ChIPQC/HCA_chipqc_meta_final.csv")[c(3:8),]
config <- data.frame(minQCth=30, fragmentSize=c(104,167,200,103,103,204), bCorPlot=T, th=0.05)
grey <- import.bed("../01c_greyLists/WT_greyList.bed")
trmB <- dba(sampleSheet = meta, peakFormat = "bed", minOverlap = 0.75, config = config)

returns the error r Error in if (res$config$bCorPlot) { : the condition has length > 1 This persists with R 4.2.1 on separate machines. Traceback returns the dba() function call. This issue is resolved when I revert to R 4.1.2 and DiffBind 3.4.11. Has anyone else encountered this error and found a work around in the current release?

R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

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

other attached packages:
 [1] DiffBind_3.6.3              SummarizedExperiment_1.26.1 Biobase_2.56.0              MatrixGenerics_1.8.1        matrixStats_0.62.0         
 [6] rtracklayer_1.56.1          GenomicRanges_1.48.0        GenomeInfoDb_1.32.2         IRanges_2.30.0              S4Vectors_0.34.0           
[11] BiocGenerics_0.42.0         openxlsx_4.2.5              forcats_0.5.1               stringr_1.4.0               dplyr_1.0.9                
[16] purrr_0.3.4                 readr_2.1.2                 tidyr_1.2.0                 tibble_3.1.8                ggplot2_3.3.6              
[21] tidyverse_1.3.2            

loaded via a namespace (and not attached):
  [1] amap_0.8-18              googledrive_2.0.0        colorspace_2.0-3         deldir_1.0-6             rjson_0.2.21             hwriter_1.3.2.1         
  [7] ellipsis_0.3.2           XVector_0.36.0           fs_1.5.2                 rstudioapi_0.14          bit64_4.0.5              ggrepel_0.9.1           
 [13] mvtnorm_1.1-3            apeglm_1.18.0            fansi_1.0.3              lubridate_1.8.0          xml2_1.3.3               codetools_0.2-18        
 [19] knitr_1.40               jsonlite_1.8.0           Rsamtools_2.12.0         broom_1.0.1              ashr_2.2-54              dbplyr_2.2.1            
 [25] png_0.1-7                GreyListChIP_1.28.1      BiocManager_1.30.18      compiler_4.2.1           httr_1.4.4               backports_1.4.1         
 [31] assertthat_0.2.1         Matrix_1.4-1             fastmap_1.1.0            gargle_1.2.0             limma_3.52.2             cli_3.3.0               
 [37] htmltools_0.5.3          tools_4.2.1              coda_0.19-4              gtable_0.3.1             glue_1.6.2               GenomeInfoDbData_1.2.8  
 [43] systemPipeR_2.2.2        ShortRead_1.54.0         Rcpp_1.0.9               bbmle_1.0.25             cellranger_1.1.0         vctrs_0.4.1             
 [49] Biostrings_2.64.0        xfun_0.31                rvest_1.0.3              irlba_2.3.5              lifecycle_1.0.1          restfulr_0.0.15         
 [55] gtools_3.9.3             XML_3.99-0.10            googlesheets4_1.0.1      MASS_7.3-58              zlibbioc_1.42.0          scales_1.2.1            
 [61] vroom_1.5.7              BSgenome_1.64.0          hms_1.1.2                parallel_4.2.1           RColorBrewer_1.1-3       yaml_2.3.5              
 [67] emdbook_1.3.12           bdsmatrix_1.3-6          SQUAREM_2021.1           latticeExtra_0.6-30      stringi_1.7.8            BiocIO_1.6.0            
 [73] caTools_1.18.2           zip_2.2.0                BiocParallel_1.30.3      truncnorm_1.0-8          rlang_1.0.4              pkgconfig_2.0.3         
 [79] bitops_1.0-7             invgamma_1.1             evaluate_0.16            lattice_0.20-45          GenomicAlignments_1.32.1 htmlwidgets_1.5.4       
 [85] bit_4.0.4                tidyselect_1.1.2         plyr_1.8.7               magrittr_2.0.3           R6_2.5.1                 gplots_3.1.3            
 [91] generics_0.1.3           DelayedArray_0.22.0      DBI_1.1.3                pillar_1.8.1             haven_2.5.0              withr_2.5.0             
 [97] mixsqp_0.3-43            RCurl_1.98-1.8           modelr_0.1.9             crayon_1.5.1             interp_1.1-3             KernSmooth_2.23-20      
[103] utf8_1.2.2               tzdb_0.3.0               rmarkdown_2.16           jpeg_0.1-9               locfit_1.5-9.6           grid_4.2.1              
[109] readxl_1.4.0             reprex_2.0.2             digest_0.6.29            numDeriv_2016.8-1.1      munsell_0.5.0
DiffBind ChIPQC • 1.5k views
Entering edit mode
Rory Stark ★ 5.1k
Last seen 4 weeks ago
Cambridge, UK

There is an error in the documentation. The config parameter should be of type list (not data.frame).

I've checked in a fix for the man page, and included a link to ?'DBA-config' which contains all supported configuration options.


Login before adding your answer.

Traffic: 799 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6