axtForSelectedDistances: Extracts pairs of genes from a CDS multiple sequence...

In asishallab/GeneFamilies: Analyses different properties of gene families

Extracts pairs of genes from a CDS multiple sequence alignment. The ones extracted are identified by computing all pairwise sequence based distances from the multiple sequence alignment. Then those pairs representing the argument statistics, e.g. 'min', 'mean', 'median', and 'max' are used to generate the axt file for subsequent analysis with KaKs_Calculator (https://sourceforge.net/projects/kakscalculator2/).

Description

Extracts pairs of genes from a CDS multiple sequence alignment. The ones extracted are identified by computing all pairwise sequence based distances from the multiple sequence alignment. Then those pairs representing the argument statistics, e.g. 'min', 'mean', 'median', and 'max' are used to generate the axt file for subsequent analysis with KaKs_Calculator (https://sourceforge.net/projects/kakscalculator2/).

Usage

axtForSelectedDistances(cds.msa, background.genes = NULL,
  dist.stats = getOption("GeneFamilies.cds.msa.dist.stats", c("min",
  "median", "mean", "max")))

Arguments

cds.msa	The result of invoking seqinr::read.alignment representing the multiple alignment of coding sequences.
background.genes	A character vector or NULL specifying a subset of the genes in argument cds.msa. If such a background is specified sequence based distances are only considered for pairs of genes where one member is taken from the background and the other from the non-background (foreground) subsets. Default is NULL.
dist.stats	A character vector holding the names of the statistics functions that are to be matched with the respective pairwise sequence based distances. Default is getOption('GeneFamilies.cds.msa.dist.stats', c('min', 'median', 'mean', 'max')).

Value

A named list. Names are those of argument dist.stats. These names can be concatonated with the letter '&' if a pair of genes fulfills the criterion of various statistics. Values are the gene pairs themselfes. Returns NA if and only if no numeric finite non-NA sequence based pairwise distances could be obtained from the multiple alignment.

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.