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 1.18.0 Index]