contiBAIT (version 1.0.0)

reorientLinkageGroups,LinkageGroupList,StrandStateMatrix-method: reorientLinkageGroups uses a simple dissimilarity to find misoriented fragments within linkage groups.

Description

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

Usage

## S3 method for class 'LinkageGroupList,StrandStateMatrix':
reorientLinkageGroups(object,
  allStrands, previousOrient = NULL, 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.

previousOrient

data.frame of type OrientationFrame of previous orientation states if performed. Default is NULL

verbose

Outputs information to the terminal. Default is TRUE.

Value

• 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)

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