ctk_tag2profile: Wrapper function for ctk's ctk_tag2profile

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Wrapper function for ctk's ctk_tag2profile

Description

Wrapper function for ctk's ctk_tag2profile

Usage

ctk_tag2profile(
  filesToRun,
  outFile = paste0(file_path_sans_ext(filesToRun), ".out"),
  outFile2 = NULL,
  sb = "tag2profile.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  bigFile = FALSE,
  weight = FALSE,
  weightAvg = FALSE,
  ss = TRUE,
  exact = TRUE,
  nz = FALSE,
  ext5 = NULL,
  ext3 = NULL,
  chromLen = NULL,
  region = NULL,
  minBlockSize = 2e+06,
  windowSize = 100,
  stepSize = 20,
  outputFormat = "bedgraph",
  normalization = "none",
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_tag2profile_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_tag2profile_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).
outFile2	path to output 2 file (BED; specify two output files to separate strands).
sb	path to tag2profile.pl from CTK.
perl	path to PERL
PATHTOPERLLIB	path to PERL5LIB.
bigFile	TRUE when working with a big file, TRUE or FALSE (default).
weight	weight counts according to the score of each tag, TRUE or FALSE (default).
weightAvg	weight average the score of each tag, TRUE or FALSE (default).
ss	separate strand, TRUE (default) or FALSE.
exact	exact count at each nucleotide, TRUE (default) or FALSE.
nz	don't print zeroes (works for sgr and bed), TRUE or FALSE (default).
ext5	extension of tags at the 5' end, default is NULL (set to integer to specify).
ext3	extension of tags at the 3' end, default is NULL (set to integer to specify).
chromLen	chrom length file, default is NULL (set file path to specify).
region	a bed file with regions to count tag numbers; if not specified (NULL), count in moving windows
minBlockSize	minimum number of lines to read in each block for a big file, default is 2000000.
windowSize	window size, default is 100.
stepSize	step size, default is 20.
outputFormat	output format, "bed" or "bedgraph" (default) or "sgr".
normalization	normalization, "none" (default) or "rpkm" or multiply=1.3).
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.

Author(s)

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",verbose=TRUE)
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,verbose=TRUE)
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)
myCollaped <- ctk_tag2collapse(parsedAlignment,weight=FALSE,randomBarcode=FALSE,
weightInName=FALSE,verbose=TRUE)
myrgbBed <- ctk_bed2rgb(myCollaped,col="128,0,0")
ctk_tag2profile(myrgbBed,verbose=TRUE)

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