getEmissionProb: Get the emission distribution parameters.

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

Description

This function accesses the emission distribution parameters of the TFFM.

Usage

  getEmissionProb(tffm)

Arguments

tffm	A TFFMFirst object or a TFFMDetail object.

Details

This function accesses the emission distribution parameters for each position of the TFFM. It returns the probability of emitting certain nucleotide based on the nucleotide on the previous site.

Value

A matrix of numeric with dimensions of 16 * ncol(tffm).

Author(s)

Ge Tan

See Also

getPosProb

Examples

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

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