DeepG4InputFromBED: Pre-Computing function of DeepG4. To use before DeepG4 main...

In morphos30/DeepG4: A deep learning approach to predict active G-quadruplexes

Pre-Computing function of DeepG4. To use before DeepG4 main function

Description

Pre-Computing function of DeepG4. To use before DeepG4 main function

Usage

DeepG4InputFromBED(
  BED = NULL,
  ATAC = NULL,
  is.bw = TRUE,
  GENOME = NULL,
  use.bg = TRUE,
  windows_bg = 5000,
  treshold_bg = 2
)

Arguments

BED	An object of class GRanges.
ATAC	A character path of bigWig/bedGraph file, or an object of class GRanges/SimpleRleList.
is.bw	a boolean. Set to TRUE if you want to use rtracklayer::import.bw fonction, FALSE use rtracklayer::import.bedGraph.
GENOME	a BSgenome object containing the DNA sequence of genome of interest.
use.bg	a boolean. Set to TRUE you want to normalize the accessibility using a windows background of windows_bg.
windows_bg	numeric value who define the windows use to get background signal.
treshold_bg	numeric value who set the treshold signal/background.

Value

a list(DNAStringSet,vector) with fasta sequence from GENOME of BED, and vector of accessibility of BED.

morphos30/DeepG4 documentation built on June 11, 2022, 10:38 p.m.