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oddmund.nordgard
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@oddmundnordgard-23558
Last seen 4.6 years ago
I am trying to make an oncoplot with the oncoplot function of the maftools package (version 2.4.0), using R version 4.0.0. Everything is fine as long as I don't try to plot the nonmutated samples. But when I call:
> oncoplot(maftest,removeNonMutated=FALSE)
Error in top_bar_data[, colnames(numMat), drop = FALSE] :
subscript out of bounds
....I get the error message above. My MAF file contains nonmutated samples, having just a name, but otherwise empty. Is there an issue with the format of those nonmutated rows in the MAF file or have I found a bug? I did not experiece this message with a previous version of R/BionConductor and maftools.
sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux
Matrix products: default
BLAS: /usr/lib/libblas.so.3.9.0
LAPACK: /usr/lib/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.utf8
[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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] maftools_2.4.0
loaded via a namespace (and not attached):
[1] compiler_4.0.0 Matrix_1.2-18 tools_4.0.0 RColorBrewer_1.1-2
[5] survival_3.1-12 splines_4.0.0 grid_4.0.0 data.table_1.12.8
[9] lattice_0.20-41