Wrapper function for ctk's getMutationType

ctk_getMutationType(
  filesToRun,
  outFile = paste(file_path_sans_ext(fileToRun), mutationType, "bed", sep = "."),
  sb = "getMutationType.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  mutationType = "del",
  summaryStat = FALSE,
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_getMutationType_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_getMutationType_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE,
  writelog = T
)

Arguments

filesToRun: path to file to process (BED).
outFile: output file (BED).
sb: path to ctk_getMutationType.pl from CTK toolkit.
perl: path to PERL.
PATHTOPERLLIB: path to PERL5LIB.
mutationType: mutation type, "del" (deletions; default),"ins" (insertions), "sub" (substitutions).
summaryStat: create summary file, TRUE or FALSE (default).
stderr: path to stdout file.
stdout: path to stdout file.
useClipRConda: use conda environment installed by Herper, TRUE (default) or FALSE.
additional_Args: additional arguments to be passed to system call.
verbose: print messages, TRUE or FALSE (default).
writelog: write stderr/stdout logs, TRUE (default) or FALSE.

Value

path to getMutationType bed file.

Author

Kathryn Rozen-Gagnon

Examples

mutations <- system.file("extdata/BrdU.Fox.pool.tag.uniq.mutation.small.txt",package="CLIPflexR")
ctk_getMutationType(mutations)
#> [1] "/Users/runner/work/_temp/Library/CLIPflexR/extdata/BrdU.Fox.pool.tag.uniq.mutation.small.del.bed"