curateIntrons: Internal function for excluding low mappability regions from...

In lbroseus/SIRFindeR: More stable and accurate estimation of Intron Retention levels

Description

This function removes low mappability regions from intronic intervals. Blacklisted regions are those having mappability score below a given threshold and spanning a minimal width (eg: read length). In certain cases (depending on read length and your reference genome) pre-computed mappability scores can be downloaded from ENCODE databases.

Usage

curateIntrons(
  mappabilityFile = NULL,
  chainPath = NULL,
  readLength,
  minMapScore = 0.5,
  saveDir,
  verbose = TRUE
)

Arguments

mappabilityFile	Path to the (bed?) file containing mappability score to use. If NULL, no mappability curation will be performed (Default: NULL).
chainPath	(Default: NULL). A Chain object, usually imported with ['import.chain'], or something coercible to one. Specify only if genome version liftover of mappability scores is needed.
readLength	Consider only low mappability region longer than this value.
minMapScore	Masq regions with mappability score below this value (Default: 0.5)
saveDir	Path to the directory where all sample results are saved.
verbose	Whether information messages should be displayed (DEFAULT: TRUE).

Value

A GRangesList having same length as indIntrons listing sub-intervals with mappability score and width above the specified thresholds.

lbroseus/SIRFindeR documentation built on Nov. 30, 2020, 11:06 a.m.