parseMemeBranchResults: Parses a HyPhy MEME branch result file to extract significant...

In asishallab/GeneFamilies: Analyses different properties of gene families

Parses a HyPhy MEME branch result file to extract significant LEAVES with codons showing signs of positive selection.

Description

Parses a HyPhy MEME branch result file to extract significant LEAVES with codons showing signs of positive selection.

Usage

parseMemeBranchResults(meme.file, bayes.factor.sign.cutoff = 100,
  fam.name.reg.exp = "/(fam\\d+)/")

Arguments

meme.file	a valid file path to a MEME branch result file, e.g. 'fam8119_hyphy_meme_output.txt.branches'
bayes.factor.sign.cutoff	The numeric value above which to consider a Bayes-Factor to be significant. Default is highly conservative and set to 100 aka 'decisive'
fam.name.reg.exp	The regular expression used within base::regexec(...) to extract the gene family's name from the meme.file argument

Value

A data.frame with four columns: Family, Site, Branch, and BayesianFactor, where the rows hold the significant results. NULL is returned if no significant results were contained in meme.file.

asishallab/GeneFamilies documentation built on July 28, 2024, 11:44 a.m.