fetchSequencesForClIP: Retrieve sequences from under peaks/regions

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Retrieve sequences from under peaks/regions

Description

Retrieve sequences from under peaks/regions

Usage

fetchSequencesForCLIP(
  peaks,
  resize = NULL,
  fasta,
  add5 = 0,
  add3 = 0,
  verbose = FALSE,
  bedHeader = TRUE,
  bedSep = "\t"
)

Arguments

peaks	CLIP peaks to process; accepts path to peak files (BED file or BED-formatted tab-delimited text files) or R objects (GRanges or BED-formatted data.frame); peak locations must be unique.
resize	size of window in bp for resizing around peak center, default is NULL (set by specifying integer).
fasta	path to genome file (fasta).
add5	bp to add to 5' of resized peak, default is 0 (set by specifying integer).
add3	bp to add to 3' of resized peak, default is 0 (set by specifying integer).
verbose	print messages, TRUE or FALSE (default).
bedHeader	if peak file contains column headers, TRUE (default) or FALSE; if TRUE, column names must be "seqnames" (chromosome), "start" (peak start), "end" (peak end), "strand" (peak strand).
bedSep	separator in BED file.

Value

path to unzipped file.

Author(s)

Kathryn Rozen-Gagnon

Examples

 
testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
decom <- decompress(testFQ,overwrite=TRUE)
com <- compress(decom,overwrite=TRUE)

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