kmerSplit: Split gene groups based on similarity

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

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)

• pgVirtual: Kmer similarity based group splitting for pgVirtual subclasses

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)

thomasp85/FindMyFriends documentation built on April 25, 2020, 1:06 p.m.