GetWTandMutCount #14
Description
Hi,
I am trying to run Battenberg but I get an error from this function runGetDirichletProcessInfo. Could you help me understand and solve the problem?
>runGetDirichletProcessInfo(loci_file="foo.txt", allele_frequencies_file="bar.txt", cellularity_file="c.txt",subclone_file="s.txt",output_file="o.txt",gender="male", SNP.phase.file=NA,mut.phase.file=NA)
Error in if (is.na(subs.data)) { : the condition has length > 1
I could trace it back to GetWTandMutCount here is the part of the code in this repo:
GetWTandMutCount <- function(loci_file, allele_frequencies_file) {
subs.data = tryCatch(read.table(loci_file, sep='\t', header=F, stringsAsFactors=F), error=function(e) NA)
if (is.na(subs.data)) {
# Empty input
return(NULL)
}
subs.data = subs.data[order(subs.data[,1], subs.data[,2]),]
#...
#...
When I try it:
>subs.data = tryCatch(read.table("foo_loci.txt", sep='\t', header=F, stringsAsFactors=F), error=function(e) NA)
#it is not empty
> head(subs.data)
V1 V2 V3 V4
1 1 653452 T C
2 1 653927 A G
3 1 962261 C T
4 1 996120 C T
5 1 1131436 A G
6 1 1131439 A G
> if (is.na(subs.data)) {
# Empty input
return(NULL)
}
Error in if (is.na(subs.data)) { : the condition has length > 1
> head(is.na(subs.data))
V1 V2 V3 V4
[1,] FALSE FALSE FALSE FALSE
[2,] FALSE FALSE FALSE FALSE
[3,] FALSE FALSE FALSE FALSE
[4,] FALSE FALSE FALSE FALSE
[5,] FALSE FALSE FALSE FALSE
[6,] FALSE FALSE FALSE FALSE
Thank you!
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)