annotationBasedShannonEntropy: Compute Shannon Entropy ('entropy') as a measure of...

In asishallab/GeneFamilies: Analyses different properties of gene families

Compute Shannon Entropy (entropy) as a measure of annotation (function) diversity within a given set of genes. If gene(s) have multiple annotations these are sorted and concatonated in order to treat them as single composite annotations. This means, that e.g if all genes have the same three annotations the resulting entropy will be 0.

Description

Compute Shannon Entropy (entropy) as a measure of annotation (function) diversity within a given set of genes. If gene(s) have multiple annotations these are sorted and concatonated in order to treat them as single composite annotations. This means, that e.g if all genes have the same three annotations the resulting entropy will be 0.

Usage

annotationBasedShannonEntropy(gene.accs, gene.annos = all.ipr,
  gene.col = 1, anno.col = 2,
  entropy.funk = getOption("GeneFamilies.entropy.function",
  entropy::entropy))

Arguments

gene.accs	The identifiers or accessions of the genes to compute the entropy for
gene.annos	The data.frame holding the annotations for the genes in 'gene.accs'. Default is all available InterPro annotations expected to be found in 'all.ipr'
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
entropy.funk	The function to be used to compute the Shannon Entropy. Default is getOption( 'GeneFamilies.entropy.function', entropy::entropy ). Set to GeneFamilies::shannonEntropy if you want normalized Shannon Entropy. See Entropy Explorer R package.

Value

A list with two entries: 'entropy' is the computed shannon entropy, and 'gene.annos.freqs' is an instance of table showing the annotation architectures and their frequencies

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