kmerSplit {FindMyFriends}R Documentation

Split gene groups based on similarity

Description

This function splits up gene groups based on cosine similarity of kmer feature vectors. It uses hard splitting based on a similarity cutoff where unconnected components constitutes new groups. Unlike neighborhoodSplit, paralogues cannot be forced into separate groups as information needed for this is not present.

Usage

kmerSplit(object, ...)

## S4 method for signature 'pgVirtual'
kmerSplit(object, kmerSize, lowerLimit, maxLengthDif,
  pParam)

Arguments

object

A pgVirtual subclass

...

Arguments passed on

kmerSize

The length of kmers used for sequence similarity

lowerLimit

The lower limit of sequence similarity below which it will be set to 0

maxLengthDif

The maximum deviation in sequence length to allow. Between 0 and 1 it describes a percentage. Above 1 it describes a fixed length

pParam

An optional BiocParallelParam object that defines the workers used for parallelisation.

Value

A new pgVirtual subclass object of the same class as 'object'

Methods (by class)

See Also

Other group-splitting: neighborhoodSplit

Examples

# Get a grouped pangenome
pg <- .loadPgExample(withGroups = TRUE)

## Not run: 
# Split groups by similarity (Too heavy to include)
pg <- kmerSplit(pg, lowerLimit = 0.8)

## End(Not run)


[Package FindMyFriends version 1.12.0 Index]