DiffBind dba.count error Error in if (sum(tokeep) < length(tokeep))

Question

[wangxiong]

When I used dba.cout with DiffBind， the following error occurred.

dbObj <- dba(sampleSheet="SampleSheet.csv") FAD1 AD 1 narrow FAD2 AD 2 narrow WT1 WT 1 narrow WT2 WT 2 narrow dbObj <- dba.count(dbObj, bUseSummarizeOverlaps=TRUE) Computing summits... Re-centering peaks... Error in if (sum(tokeep) < length(tokeep)) { : missing value where TRUE/FALSE needed

I have tried in Rstudio server or R in linux, both failed. I have attached the dir of files and the SampleSheet.csv

Here is the head of bed file

[wangxiong]

Can anyone help?

[Rory Stark]

Can you confirm the version you are using (sessionInfo())?

Also, if you can try setting filter=0 in the call to dba.count(), it would be informative to know if that worked.

[wangxiong]

R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS

Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

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

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

loaded via a namespace (and not attached): [1] compiler_4.1.1 fastmap_1.1.0 htmltools_0.5.2 tools_4.1.1 yaml_2.2.1 rmarkdown_2.11 [7] knitr_1.37 xfun_0.29 digest_0.6.29 rlang_0.4.12 evaluate_0.14

> dbObj <- dba.count(dbObj, bUseSummarizeOverlaps=TRUE,filter=0)
Computing summits...
Re-centering peaks...
Error in if (sum(tokeep) < length(tokeep)) { : 
  missing value where TRUE/FALSE needed

[Rory Stark]

I still don't see the DiffBind version in this posting? What does package.version("DiffBind") return?

If you don't mind, I'll continue the response to this at the duplicated entry on the Bioconductor support forum: https://support.bioconductor.org/p/9141572/#9141598

Check there for more information.