ctk_cims: Wrapper function for ctk's CIMS
In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

ctk_cims

R Documentation

Wrapper function for ctk's CIMS

Description

Wrapper function for ctk's CIMS

Usage

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(s)

Kathryn Rozen-Gagnon

Examples

## Not run: 
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)

## End(Not run)

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.