Output GenVisR mutation frequency data by gene name instead of sample name

[Sheneice.c]

Hi,
I would like to know using package GenVisR, is it possible to output the mutation frequency data from waterfall function to data by gene instead of sample by default? Using writeData function within GenVisR package creates error which I couldn't resolve. Here is the code i used:

writeData(waterfall(mutationData, mainRecurCutoff = 0.05, mainPalette 
                    = mycolors, clinData = Clin_Data1, maxGenes = 30,
                    rmvSilent = TRUE, fileType = "Custom", out = "data",
                    variant_class_order = mutation_priority), file("Test.csv"))
#> Error in writeData(waterfall(mutationData, mainRecurCutoff = 0.05, mainPalette = mycolors, : could not find function "writeData"

This is the error when i tried to run my code:

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘writeData’ for signature ‘"list"’

I succesfully plotted the waterfall plot using the package but I would like to get the mutation frequency data by gene name (which is plotted in subplot) in table for analysis. Welcome any comments or suggestions, thank you in advance!

[jcblum]

Hi @Sheneice.c! Welcome!

Since GenVisR is a Bioconductor package, you might have more luck posting on the Bioconductor support forums. (These packages can get pretty specialized, and it’s possible there are very few people here who have used this specific package before).

Please be sure to read the Bioconductor posting guide before you ask your question:
https://www.bioconductor.org/help/support/posting-guide/