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

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Description

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

Usage

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## 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 data.frame of type OrientationFrame containing contig names and orientations, as '+' or '-' and a merged LinkageGroupList.

Examples

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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

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