kmerLink {FindMyFriends} | R Documentation |
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.
kmerLink(object, ...) ## S4 method for signature 'pgVirtual' kmerLink(object, lowMem, kmerSize, lowerLimit, rescale, transform, pParam, algorithm, ...)
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 |
An object with the same class as object with linking between gene groups.
pgVirtual
: Linking for pgVirtual subclasses
testPG <- .loadPgExample(withGroups=TRUE) # No paralogue links hasParalogueLinks(testPG) # Create the links testPG <- kmerLink(testPG)