replace_bg: Replace the control regions with user provided background.

In exomePeak2: Bias Awared Peak Calling and Quantification for MeRIP-Seq

Description

Replace the control regions with user provided background.

Usage

replace_bg(grl, bg, txdb)

Arguments

grl	A GRangesList of the merged peaks which the background regions are waiting to be replaced.
bg	A GRanges or GRangesList object of the user provided background.
txdb	A TxDb object that define the transcript annotation.

Value

A GRangesList object. The first portion is the exons regions that is not overlapped with annoation.

If the resulting ranges have less number and width compared with what defined in cut_off_width or cut_off_num, the exon regions of txdb will be returned as the background.

The second portion is the restructed user provided annotation with gene id annotated.

exomePeak2 documentation built on Nov. 8, 2020, 5:27 p.m.