GetWTandMutCount

[rabiafidan]

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)

[rabiafidan]

I have just noticed #10 is also the same issue.

[rabiafidan]

I found empty_input_bugfix branch while browsing and it worked for me:

remove.packages("dpclust3p")
devtools::install_github("Wedge-Oxford/dpclust3p",ref="empty_input_bugfix")

[christopherwirth]

Hi Rabia,

Thanks for the comments and error messages. Apologies we weren't able to respond sooner; I was on annual leave.

Is the bugfix branch still working for you generally?

If so, I will coordinate with the team and see if we can merge it into the master branch before I close this issue.

[rabiafidan]

Hi Chris,

Thank you for your reply. I haven't had the chance to test it further but it had worked on 1 sample. I would like to run it on a cohort soon. I can update here then but all seems fine.

[rabiafidan]

Hi again,
The cohort run is also successful.