Oncoplot user error or bug?
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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
maftools • 868 views
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