dot-callDeepG4ScanATAC: Scanning of potential active G4 on a sequence or a list of...
In morphos30/DeepG4: A deep learning approach to predict active G-quadruplexes

.callDeepG4ScanATAC

R Documentation

Scanning of potential active G4 on a sequence or a list of sequences using a sliding window of size k.

Description

Scanning of potential active G4 on a sequence or a list of sequences using a sliding window of size k.

Usage

.callDeepG4ScanATAC(
  X = NULL,
  X.ATAC = NULL,
  k = 20,
  treshold = 0.5,
  threads = 1,
  lower.case = F,
  GENOME = NULL,
  use.bg = T,
  windows_bg = 5000,
  treshold_bg = 2
)

Arguments

`X`	An object of class GRanges.
`X.ATAC`	An object of class GRanges containing DNA accessibility.
`k`	size of the sliding windows.
`treshold`	numeric value who define the treshold to use to consider a sequence asc ontaining an active G4.
`threads`	numeric value who define the number of threads used in DeepG4Scan (Generate sub sequences)
`lower.case`	a boolean. Set to `TRUE` if elements of X are in lower case (default to FALSE).
`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.