getPosProb: Get the emission probabilities of nucleotides

In TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

Description

Get the emission probabilities of ACGT at each position of TFFM.

Usage

  getPosProb(tffm)

Arguments

tffm	A TFFMFirst object or a TFFMDetail object.

Details

This function calculates the probabilities of emitting nucleotides ACGT at each position of TFFM.

Value

A matrix of numeric with dimensions of 4 * ncol(tffm).

Author(s)

Ge Tan

See Also

getEmissionProb

Examples

  xmlFirst <- file.path(system.file("extdata", package="TFBSTools"),
                        "tffm_first_order.xml")
  tffmFirst <- readXMLTFFM(xmlFirst, type="First")
  getPosProb(tffmFirst)
  
  xmlDetail <- file.path(system.file("extdata", package="TFBSTools"),
                         "tffm_detailed.xml")
  tffmDetail <- readXMLTFFM(xmlDetail, type="Detail")
  getPosProb(tffmDetail)

TFBSTools documentation built on Nov. 8, 2020, 8:14 p.m.