Wrapper function for ctk's bed2rgb

ctk_bed2rgb(
  filesToRun,
  outFile = paste0(file_path_sans_ext(filesToRun), ".RGB.", file_ext(filesToRun)),
  sb = "bed2rgb.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  col = "blue",
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_bed2rgb_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_bed2rgb_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: path to output file (BED).
sb: path to bed2rgb.pl from CTK.
perl: path to PERL.
PATHTOPERLLIB: path to PERL5LIB.
col: color to include in BED rgb column (default is "blue").
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 BED file with color specified.

Author

Kathryn Rozen-Gagnon

Examples

testFasta <- system.file("extdata/hg19Small.fa",package ="CLIPflexR")
myIndex <-suppressWarnings(bowtie2_index(testFasta, overwrite = TRUE))
testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package ="CLIPflexR")
FqFile_FF <- ctk_fastqFilter(testFQ,qsFilter="mean:0-29:20")
FqFile <- decompress(FqFile_FF,overwrite=TRUE)
FqFile_clipped <- fastx_clipper(FqFile,length=20)
FqFile_QF <- fastq_quality_trimmer(FqFile_clipped)
FqFile_Col <- ctk_fastq2collapse(FqFile_QF)
FqFile_QFColStripped <- ctk_stripBarcode(FqFile_Col,linkerlength=5,inputFormat="fastq")
bam <- suppressWarnings(bowtie_align(FqFile_QFColStripped,myIndex, 
overwrite=TRUE, inputFormat="fastq"))
parsedAlignment <- ctk_parseAlignment(bam)
myCollapsed <- ctk_tag2collapse(parsedAlignment,weight=FALSE,randomBarcode=FALSE,
weightInName=FALSE,verbose=TRUE)
#> tag2collapse.pl command is /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/tag2collapse.pl
#> tag2collapse.pl arguments are /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/tag2collapse.pl  --keep-tag-name   --keep-max-score   -EM -1  --seq-error-model em-local  /Users/runner/work/_temp/Library/CLIPflexR/extdata/Collapsed_QT_FF_Fox3_Std_small_clip_rm5.bed  /Users/runner/work/_temp/Library/CLIPflexR/extdata/TC_Collapsed_QT_FF_Fox3_Std_small_clip_rm5.bed 
ctk_bed2rgb(myCollapsed,col="128,0,0")
#> [1] "/Users/runner/work/_temp/Library/CLIPflexR/extdata/TC_Collapsed_QT_FF_Fox3_Std_small_clip_rm5.RGB.bed"