geneGroupsAnnotationBasedShannonEntropy: Computes for each gene group in 'groups.ids' the annotation...

In asishallab/GeneFamilies: Analyses different properties of gene families

Computes for each gene group in groups.ids the annotation based Shannon Entropy in parallel. Set options(mc.cores=detectCores()) for maximum speed.

Description

Computes for each gene group in groups.ids the annotation based Shannon Entropy in parallel. Set options(mc.cores=detectCores()) for maximum speed.

Usage

geneGroupsAnnotationBasedShannonEntropy(groups.ids, groups.2.genes.lst,
  gene.annos = all.ipr, gene.col = 1, anno.col = 2)

Arguments

groups.ids	The IDs of the gene groups to compute the annotation based Shannon Entropy for.
groups.2.genes.lst	A list with names intersecting with argument groups.ids and values character vectors holding gene-IDs found in gene.annos.
gene.col	the column of 'gene.annos' in which to lookup the gene identifiers or gene accessions. Default is 1
anno.col	the column of 'gene.annos' in which to lookup the function annotation for the genes in 'gene.accs'. Default is 2

Value

A list with names groups.ids and values the computed annotation based Shannon Entropies.

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