kmerLink: Link gene groups by homology

In FindMyFriends: Microbial Comparative Genomics in R

Description

This method allows the user to define a secondary grouping of genes be linking gene groups based on sequence similarity (paralogues). A representative for each gene group is used for the calculations and the similarity is assessed using the kmer based cosine similarity.

Usage

kmerLink(object, ...)

## S4 method for signature 'pgVirtual'
kmerLink(object, lowMem, kmerSize, lowerLimit,
  rescale, transform, pParam, algorithm, ...)

Arguments

object	A pgVirtual subclass
...	parameters passed on to the community detection algorithm.
lowMem	logical. Should low memory footprint be ensured over computation speed
kmerSize	The size of kmers to use for similarity calculations.
lowerLimit	The lower threshold for similarity below which it is set to 0
rescale	Should Similarities be normalised between lowerLimit and 1
transform	Transformation function to apply to similarities
pParam	An optional BiocParallelParam object that defines the workers used for parallelisation.
algorithm	The name of the community detection algorithm from igraph to use for gene grouping. See communities for an overview. The trailing '.community' can be omitted from the name. Default is 'infomap', which is also the recommended.

Value

An object with the same class as object with linking between gene groups.

Methods (by class)

• pgVirtual: Linking for pgVirtual subclasses

Examples

testPG <- .loadPgExample(withGroups=TRUE)

# No paralogue links
hasParalogueLinks(testPG)

# Create the links
testPG <- kmerLink(testPG)

FindMyFriends documentation built on Nov. 8, 2020, 6:46 p.m.