reorientAndMergeLGs,LinkageGroupList,StrandStateMatrix-method {contiBAIT} | R Documentation

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

### 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

[Package contiBAIT version 1.16.0 Index]