importMatrix: import motifs from local files

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

import motifs from local files

Description

Import the motifs into pcm-class or pfm-class from files exported from Transfac, CisBP, and JASPAR.

Usage

importMatrix(
  filenames,
  format = c("auto", "pfm", "cm", "pcm", "meme", "transfac", "jaspar", "scpd", "cisbp",
    "psam", "xmatrix"),
  to = c("auto", "pcm", "pfm", "pssm", "psam")
)

Arguments

filenames	filename, an XMatrixList object, or an XMatrix object to be imported.
format	file format
to	import to pcm-class or pfm-class

Value

a list of object pcm-class or pfm-class

Author(s)

Jianhong Ou

Examples

  path <- system.file("extdata", package = "motifStack")
  importMatrix(dir(path, "*.pcm", full.names = TRUE))

jianhong/motifStack documentation built on Jan. 31, 2024, 5:03 a.m.