Wrapper function for ctk's CITS

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

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")