exprVecSpaceEvolutionAfterDupl: Based on an expression vector space infers the evolution of...

In asishallab/GeneFamilies: Analyses different properties of gene families

Based on an expression vector space infers the evolution of gene function after duplication by comparing base genes and groups of evolved genes.

Description

Based on an expression vector space infers the evolution of gene function after duplication by comparing base genes and groups of evolved genes.

Usage

exprVecSpaceEvolutionAfterDupl(genes, family.name, classifier.lst,
  base.class = "ortholog", expr.vecs = rpkm.expr.profiles.df,
  gene.col = "gene", vec.space.axes = c("cotyledon", "seedling",
  "developing leaf", "flower stage 9", "flower stage 16"))

Arguments

genes	character vector of gene identifiers
family.name	The name of the gene group comprising argument genes
classifier.lst	A named list of at least two entries. Entries should be lists of gene IDs belonging to their respective (named) classes.
base.class	A name of argument classifier.lst to be used as base gene class. Default is 'ortholog'.
expr.vecs	A set of vectors in the respective expression vector space. Each row holds the expression vector for its respective gene. Default is rpkm.expr.profiles.df.
gene.col	The name or index of a column of argument expr.vecs indicating in which column to lookup gene IDs.
vec.space.axes	A character or integer vector indicating the columns of argument expr.vecs which correspond to the respective vector space axes. Default is c('cotyledon', 'seedling', 'developing leaf', 'flower stage 9', 'flower stage 16').

Value

A data.frame with the following columns: Family (set to argument family.name, mean.base.tiss.vers, and for each class 'EvCl' of evolved genes EvCl.tiss.vers, EvCl.tiss.change, and EvCl.dist.vec.clouds

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