Wrapper function for ctk's tag2collapse

ctk_tag2collapse(
  filesToRun,
  outFile = file.path(dirname(filesToRun), paste0("TC_", basename(filesToRun))),
  sb = "tag2collapse.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  keepMaxScore = TRUE,
  keepTagName = TRUE,
  weight = TRUE,
  bigFile = FALSE,
  weightInName = TRUE,
  randomBarcode = TRUE,
  seqErrorModel = "em-local",
  outputSeqError = NULL,
  em = NULL,
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_tag2collapse_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_tag2collapse_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

sb

path to tag2collapse.pl from CTK.

perl

path to PERL.

PATHTOPERLLIB

path to PERL5LIB.

keepMaxScore

keep the tag with the most weight (instead of the longest one) as representative.

keepTagName

do not change tag name (no extra information).

weight

consider the weight of each tag.

bigFile

Set to TRUE when files are big.

weightInName

find weight in name.

randomBarcode

random barcode exists, no collapse for different barcodes.

seqErrorModel

sequencing error model to use, "alignment" or "em-local" (default) or "em-global" or "fix=0.01".

outputSeqError

output sequencing errors estimated by the EM algorithm.

em

EM threshold to infer reliability of each collapsed read (when have random linker, -1=no EM).

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 collapsed BED file.

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",verbose=TRUE)
#> fastq_filter.pl command is /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq_filter.pl
#> fastq_filter.pl arguments are /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq_filter.pl  -if sanger  -of fastq  -f mean:0-29:20  /Users/runner/work/_temp/Library/CLIPflexR/extdata/Fox3_Std_small.fq.gz  /Users/runner/work/_temp/Library/CLIPflexR/extdata/FF_Fox3_Std_small.fq.gz 
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)
#> fastq_filter.pl command is /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq2collapse.pl
#> fastq_filter.pl arguments are /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq2collapse.pl  /Users/runner/work/_temp/Library/CLIPflexR/extdata/QT_FF_Fox3_Std_small_clip.fq  /Users/runner/work/_temp/Library/CLIPflexR/extdata/Collapsed_QT_FF_Fox3_Std_small_clip.fq 
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)
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 
#> [1] "/Users/runner/work/_temp/Library/CLIPflexR/extdata/TC_Collapsed_QT_FF_Fox3_Std_small_clip_rm5.bed"