bigwig_profile_matrix: Generate profile matrix using normalizeToMatrix()

In lakhanp1/chipmine: Analyze ChIP-seq Data

Description

Generate profile matrix using normalizeToMatrix()

Usage

bigwig_profile_matrix(
  bwFile,
  regions,
  signalName,
  extend = c(2000, 1000),
  w = 10,
  targetName = "gene",
  storeLocal = FALSE,
  localPath,
  ...
)

Arguments

bwFile	BigWig file for the signal
regions	bed file for the regions/genes of interest or a GenomicRanges object
signalName	Signal name
extend	extend argument of normalizeToMatrix function. Default: c(2000, 1000)
w	w argument of normalizeToMatrix function: Default: 10
targetName	Name to be used for target. Eg: "gene", "TSS", "TES", "summit" etc. default: gene
storeLocal	Logical. Whether to store the matrix locally as gzipped file. Default: FALSE
localPath	File path pointing to locally stored matrix
...	other arguments passed to function normalizeToMatrix function

Value

profile matrix of class normalizedMatrix

Examples

NULL

lakhanp1/chipmine documentation built on March 6, 2021, 9:06 a.m.