reorientAndMergeLGs: reorientAndMergeLGs uses a simple dissimilarity to find...

In oneillkza/ContiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

Description

reorientAndMergeLGs uses a simple dissimilarity to find misoriented fragments within linkage groups.

Usage

## S4 method for signature 'LinkageGroupList,StrandStateMatrix'
reorientAndMergeLGs(object,
  allStrands, cluster = NULL, clusterParam = NULL, similarityCutoff = 0.9,
  verbose = TRUE)

Arguments

object	List of vectors containing names of contigs belonging to each LG.
allStrands	Table of type strandStateMatrix encompassing strand state for all contigs. Product of StrandSeqFreqTable.
cluster	Number of times to recluster and take the consensus of. If NULL, clustering is run only once.
clusterParam	optional BiocParallelParam specifying cluster to use for parallel execution. When NULL, execution will be serial.
similarityCutoff	merge contigs that are more similar this this
verbose	Outputs information to the terminal. Default is TRUE.

Value

a list consisting of a strandStateMatrix (a reoriented version of allStrands), a ChrTable containing contig names and orientations, as '+' or '-' and a merged LinkageGroupList.

Examples

data(exampleLGList)
data(exampleWCMatrix)

reorientedMatrix <- reorientAndMergeLGs(exampleLGList,
										  exampleWCMatrix)

# Note that in this example data, everything is correctly oreiented to
# to begin with, so all contigs come out as + orientation

oneillkza/ContiBAIT documentation built on June 1, 2020, 5:49 a.m.