ctk_cits: Wrapper function for ctk's CITS

View source: R/wrapperFunctions_ctk.R

ctk_citsR Documentation

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.