View source: R/selection_funks.R
parseMemeBranchResults | R Documentation |
Parses a HyPhy MEME branch result file to extract significant LEAVES with codons showing signs of positive selection.
parseMemeBranchResults(meme.file, bayes.factor.sign.cutoff = 100,
fam.name.reg.exp = "/(fam\\d+)/")
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
|
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
.
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