contiBAIT (version 1.0.0)

mergeLinkageGroups,LinkageGroupList,StrandStateMatrix-method: mergeLinkageGroups -- merge very similar linkage groups, including those in reverse orientation

Description

mergeLinkageGroups -- merge very similar linkage groups, including those in reverse orientation

Usage

## S3 method for class 'LinkageGroupList,StrandStateMatrix':
mergeLinkageGroups(object,
  allStrands, clusterParam = NULL, cluster = 1, similarityCutoff = 0.7)

Arguments

object

LinkageGroupList

allStrands

StrandStateMatrix for all linkageGroups (usually reoriented by reorientStrandTable)

clusterParam

optional BiocParallelParam specifying cluster to use for parallel execution. When NULL, execution will be serial.

cluster

Integer denoting the number of reclusterings to be performed for creating linkage groups (default is 1)

similarityCutoff

merge contigs that are more similar this this

Value

• list of indices within the allStrands matrix indicating linkage group membership, a list consisting of a strandStateMatrix (a reoriented version of allStrands), and a data.frame of type OrientationFrame containing contig names and orientations, as '+' or '-'.

Examples

data(exampleWCMatrix)
clusteredContigs <- clusterContigs(exampleWCMatrix, randomise=FALSE)

reorientedMatrix <- reorientLinkageGroups(clusteredContigs,
										  exampleWCMatrix)

exampleLGList <- mergeLinkageGroups(clusteredContigs,
									reorientedMatrix[[1]])