import_profile_from_file: Read profile matrix from file

In lakhanp1/chipmine: Analyze ChIP-seq Data

Description

This function reads the locally stored profile matrix and convert it to normalizedMatrix class. This matrix can be used for generating profile plot using EnrichedHeatmap package.

Usage

import_profile_from_file(
  file,
  source = "normalizedmatrix",
  signalName,
  selectGenes,
  up = 200,
  target = 200,
  down = 100,
  binSize = 10,
  targetType = "region",
  targetName = "gene",
  keep = c(0, 1),
  returnDf = FALSE
)

Arguments

file	profile matrix for e.g. generated by deeptools' computeMatrix scale-regions command
source	A character string for the source of the matrix being read. One of "deeptools", "miao", "normalizedmatrix". Default: normalizedmatrix
signalName	name of the signal track
selectGenes	A vector of gene IDs which are to be plotted.. Only these genes' profile is extracted from the profile matrix for plotting.
up	number of bins in upstream region
target	number of bins in gene body
down	number of bins in downstream region
binSize	bin size used while generating profile matrix
targetType	One of "region", "point". If targetType is "region", target is used to decide the number of bins over region. Otherwise, for "point", a signle point matrix is expected where the region is extracted around single point. Default: region
targetName	Name to be used for target. Eg: "gene", "TSS", "TES", "summit" etc. default: gene
keep	Same as EnrichedHeatmap::normalizeToMatrix. First value is used as lower quantile and any value in profile matrix less than lower quantile is set to lower quantile. Second value is used as upper quantile and any value greater than upper quantile is set to upper quantile. Default: c(0, 1)
returnDf	If TRUE, returns the dataframe instead of profile matrix. Default: FALSE

Value

profile matrix of class normalizedMatrix

Examples

NA

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