readJASPARMatrix {TFBSTools}R Documentation

Read JASPAR format matrix

Description

Read a JASPAR format matrix file with ‘individual’ matrix or ‘all’ matrices in one file.

Usage

  readJASPARMatrix(fn, type = c("individual", "all"))

Arguments

fn

character(1): The filename of JASPAR format matrix file.

type

character(1): It can be ‘individual’ or ‘all’.

Details

An example of ‘individual’ format matrix file is available at http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/individual/MA0001.1.pfm

An exmaple of ‘all’ format matrix file is available at http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all.txt

Value

When ‘individual’, a PFMatrix object is returned. When ‘all’, a PFMatrixList object is returned.

Author(s)

Ge Tan

See Also

makeFlatFileDir

Examples

  fn <- file.path(system.file("extdata", package="TFBSTools"),
                  "MA0001.1.pfm")
  readJASPARMatrix(fn, type="individual")
  fn <- file.path(system.file("extdata", package="TFBSTools"),
                  "pfm_all_example.txt")
  readJASPARMatrix(fn, type="all")

[Package TFBSTools version 1.20.0 Index]