ExtractSubSequencefromBed: ExtractSubSequencefromBed : Internal function for DeepG4Scan.

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

ExtractSubSequencefromBed : Internal function for DeepG4Scan.

Description

ExtractSubSequencefromBed : Internal function for DeepG4Scan.

Usage

ExtractSubSequencefromBed(
  x = NULL,
  x.atac = NULL,
  k = 20,
  GENOME = NULL,
  seq.size = 201,
  nb.threads = 1,
  use.bg = T,
  windows_bg = 5000,
  treshold_bg = 2
)

Arguments

x	An object of class GRanges.
x.atac	A SimpleRleList object containing DNA accessibility.
k	size of the sliding windows.
GENOME	a BSgenome object containing the DNA sequence of genome of interest.
seq.size	numeric value representing the sequence size accepted by our model. Don't change it unless you want to use our function with a custom model.
nb.threads	number of threads to use, default 1.
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 data.frame with position of subsequence, DNA sequence and accessibility.

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