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

## mergeFlankedLGs – searches for similarities at the ends of ordered linkage groups to chain groups together

### Description

mergeFlankedLGs – searches for similarities at the ends of ordered linkage groups to chain groups together

### Usage

      ## S4 method for signature 'LinkageGroupList,StrandStateMatrix'
    mergeFlankedLGs(linkageGroupList,
      strandStateMatrix, buildConsensus = 1, cluster = NULL,
      clusterParam = NULL, similarityCutoff = 0.7, verbose = TRUE)

### Arguments

`linkageGroupList` | List of ordered vectors containing names of contigs belonging to each LG, of type LinkageGroupList
`strandStateMatrix` | Table of type strandStateMatrix encompassing strand state for all contigs. Product of StrandSeqFreqTable.
`buildConsensus` | number of contigs to take at the end of the linkage group to build a consensus strand state. Default is 5
`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 containing a revised LinkageGroupList with merged groups, if appropriate, and a StrandStateMatrix with contigs reoriented, if newly merged groups were in opposite orientations.

[Package contiBAIT version 1.22.0 Index]