readLargeBlat: Read a large blat file piece by piece

In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses

Read a large blat file piece by piece

Description

Read a large blat file piece by piece

Usage

readLargeBlat(
  fileName,
  nHeader = 5,
  nrows = 1e+06,
  isGz = grepl(".gz$", fileName),
  filterFunc = function(x) rep(TRUE, nrow(x)),
  ...
)

Arguments

fileName	name of file
nHeader	number of lines to skip at start of file
nrows	number of lines ot read in per shot
isGz	if TRUE then file is assumed to be gzipped
filterFunc	a function taking a data.frame of blat data and returning a TRUE/FALSE vector specifying rows to keep
...	additional arguments to read.blat

Value

data.frame of blat data

Warning

Assumes blat files is sorted by qName

sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.