NMF for Mutation Signatures

Question

[mingtaog]

Error in (new("standardGeneric", .Data = function (x)  :
  unused arguments (model = list("NMFstd", 2, 0), method = "random")
Calls: assessNumberSignatures ... .local -> nmf -> nmf -> nmf -> nmf -> .local -> do.call
Execution halted

[Devon Ryan]

Without seeing the command you used it's nearly impossible to help you.

[mingtaog]

setwd('path')
library(NMF)
library(SomaticSignatures)
df<-read.table('path/somatic.snv.gct',sep='\t',head=T)
dat<-df[apply(df[,c(-1,-2)],1,function(x) !all(x==0)),]
p<-data.matrix(dat[,3:ncol(dat)])
gof_nmf=assessNumberSignatures(p,2:8, nReplicates = 1) 
png("RSS.png",width=6002,height=6002,res=72*2)
plotNumberSignatures(gof_nmf)
wRSS<-data.frame(gof_nmf)
write.table(wRSS,file='RSS.txt',quote=F,row.names=F,sep='\t')
dev.off()

This is the R script. I ran it with R-v3.6.2.