annotatePeaksWithPatterns: Search for small RNA targets, or any pattern, in peaks

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Search for small RNA targets, or any pattern, in peaks

Description

Search for small RNA targets, or any pattern, in peaks

Usage

annotatePeaksWithPatterns(
  peaks,
  fasta,
  patterns,
  resize = 64,
  add5 = 0,
  add3 = 0,
  verbose = FALSE,
  exact = TRUE,
  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.
fasta	path to genome file (fasta).
patterns	patterns to scan in CLIP peaks (character vector, DNAStringSet, or file path to a fasta sequence). Ambiguous bases can be searched by using IUPAC code in the pattern sequences and setting *exact* as FALSE.
resize	size of window in bp for resizing around peak center, default is 64 (set by specifying integer; can be set to NULL to keep original peak ranges).
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).
exact	whether to search for exact matches or allow ambiguous matching, TRUE (default) or FALSE
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

Author(s)

Kathryn Rozen-Gagnon

Examples

testFasta <- system.file("extdata/hg19Small.fa",package="CLIPflexR")

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