Output GenVisR mutation frequency data by gene name instead of by sample name
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Entering edit mode
@sheneicechang-21956
Last seen 23 months ago

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? I had read the GenVisR package manual and tried to resolve using writeData function within GenVisR package, it 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"’

Using traceback() after getting the error, the consult shows:

3: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
       sQuote(fdef@generic), sQuote(cnames)), domain = NA)
2: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character, 
               ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list("list"), new("nonstandardGenericFunction", .Data = function (object, 
       ...) 
   {
       standardGeneric("writeData")
   }, generic = "writeData", package = "GenVisR", group = list(), 
       valueClass = character(0), signature = "object", default = NULL, 
       skeleton = (function (object, ...) 
       stop("invalid call in method dispatch to 'writeData' (no default method)", 
           domain = NA))(object, ...)), <environment>)
1: writeData(waterfall(mutationData, mainRecurCutoff = 0.05, mainPalette = mycolors, 
       clinData = Clin_Data1, maxGenes = 30, rmvSilent = TRUE, fileType = "Custom", 
       out = "data", variant_class_order = mutation_priority))

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

GenVisR mutation frequency R cancer bioconductor • 305 views
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