Wrapper function for ctk's CIMS

ctk_cims(
  filesToRun,
  mutationBedFile,
  outFile = paste(file_path_sans_ext(fileToRun), "CIMS", "txt", sep = "."),
  sb = "CIMS.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  bigFile = FALSE,
  mutationSize = 1,
  permutations = 5,
  trackMutationPos = FALSE,
  noSparseCorrect = FALSE,
  FDR = 1,
  mfr = 0,
  cacheDir = paste0(filesToRun, "_cache", paste(sample(letters, 10), collapse = "")),
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun), "_cims_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun), "_cims_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).
mutationBedFile: mutation BED file.
outFile: path to output file (BED & text).
sb: path to CIMS.pl from CTK.
perl: path to PERL.
PATHTOPERLLIB: path to PERL5LIB.
bigFile: big file, TRUE or FALSE (default).
mutationSize: mutation size (default is 1).
permutations: number of iterations for permutation (default is 5).
trackMutationPos: track mutation position relative to read start, TRUE or FALSE (default).
noSparseCorrect: no sparcity correction, TRUE or FALSE (default).
FDR: threshold of FDR (default is 1).
mfr: threshold of m-over-k-ratio (default is 0).
cacheDir: name for cache directory.
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 CIMS text & bed files.

Author

Kathryn Rozen-Gagnon

Examples

if (FALSE) {
mutations <- system.file("extdata/BrdU.Fox.pool.tag.uniq.mutation.small.txt",package="CLIPflexR")
delBed <- ctk_getMutationType(mutations)
ctk_cims("~/Downloads/uniq_tags_mutations/Fox.pool.tag.uniq.rgb.bed",delBed,verbose=TRUE)
}