I am analysing copy number from from a sample through VARScan2 following this manual where for doing "Segmentation and classification" I am using DNACopy and following below mentioned commands:
library(DNAcopy) cn <- read.table("your.cn.file",header=F) CNA.object <-CNA( genomdat = cn[,6], chrom = cn[,1], maploc = cn[,2], data.type = 'logratio') CNA.smoothed <- smooth.CNA(CNA.object)
but it shows me error:
Error in CNA(genomdat = cn[, 6], chrom = cn[, 1], maploc = cn[, 2], data.type = "logratio") : could not find function "CNA"
So I installed CNA by
install.packages("cna") but still received the same error.
It could be a silly fix, but it will be great if I can get some help. Thank you