disj_background {exomePeak2}R Documentation

Find the background of the user provided modification.

Description

Find the background of the user provided modification.

Usage

disj_background(
  mod_gr,
  txdb,
  background_bins = NULL,
  background_types = c("Gaussian_mixture", "m6Aseq_prior", "manual", "all"),
  control_width = 50,
  rename_mod = FALSE
)

Arguments

mod_gr

A GRanges object of user provided modification (names are neccessary for the index of the splitting).

txdb

A TxDb object that define the transcript modification.

background_bins

A Granges object for background bins.

background_types

A logical value, TRUE if the region of 5'UTR and long exons of the transcripts should be dropped in control region; Default TRUE.

control_width

A integer for the minimum width of the control region returned; default 50.

rename_mod

Whether to rename the returned modification sites, default = FALSE.

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_num, the exon regions of txdb will be returned as the background.

The second portion is the reconstructed provided modification with gene id mod_grated.


[Package exomePeak2 version 1.5.0 Index]