read.blat: Read a blat file

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

Read a blat file

Description

Read a blat file

Usage

read.blat(
  fileName,
  skips = 5,
  calcScore = TRUE,
  fixStarts = TRUE,
  nCols = 21,
  filterFunction = NULL,
  ...
)

Arguments

fileName	name of file
skips	number of lines to skip (5 for a normal blat file)
calcScore	calculate score column?
fixStarts	convert start to 1-based?
nCols	21 (no alignments) or 23 columns (alignments)
filterFunction	if not NULL then pass the output data.frame to this function and filter by logical value returned
...	additional arguments to read.table

Value

dataframe of blat data

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