ctk_cits: Wrapper function for ctk's CITS

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Wrapper function for ctk's CITS

Description

Wrapper function for ctk's CITS

Usage

ctk_cits(
  filesToRun,
  outFile = paste(file_path_sans_ext(fileToRun), "CITS", "bed", sep = "."),
  sb = "CITS.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  bigFile = FALSE,
  pCutOff = 0.01,
  multiTest = TRUE,
  gap = 25,
  cacheDir = paste0(filesToRun, "_cache", paste(sample(letters, 10), collapse = "")),
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun), "_cits_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun), "_cits_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 CITS.pl from CTK.
perl	path to PERL.
PATHTOPERLLIB	path to PERL5LIB.
bigFile	big file, TRUE or FALSE (default).
pCutOff	p-value cut off (default is 0.01).
multiTest	perform multiple testing correction, TRUE (default) or FALSE.
gap	gap size (default is 25).
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 CITS bed file.

Author(s)

Kathryn Rozen-Gagnon

Examples

testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
FqFile <- decompress(testFQ,overwrite=TRUE)
FqFile_QF <- fastq_quality_filter(FqFile)
FqFile_Col<- fastx_collapser(FqFile_QF)
FqFile_QFColStripped <- ctk_stripBarcode(FqFile_Col,linkerlength=5,inputFormat="fastq")

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