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

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

Kathryn Rozen-Gagnon

Examples

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