Hello, I have around 30 vcf files from snvs calling that I want to compare, I found a command in Rsubead package called findcommonvariants. to try this I have now 2 vcf files to compare
but I keep getting this error in normalizepath
MA01 = read.table("E:/Projects/NSCLC Brain met/NGS data/Data analysis/DNA/SNVs/MA-01.somatic.snvs.vcf", stringsAsFactors = FALSE)
MA03 = read.table("E:/Projects/NSCLC Brain met/NGS data/Data analysis/DNA/SNVs/MA-03.somatic.snvs.vcf", stringsAsFactors = FALSE))
library(Rsubread)
findCommonVariants(c('MA01','MA03'))
>Error in normalizePath(path.expand(path), winslash, mustWork) :
path[1]="MA01": The system cannot find the file specified