Retrieve sequences from under peaks/regions

Retrieve sequences from under peaks/regions

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

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)