mergeFlankedLGs: mergeFlankedLGs - searches for similarities at the ends of...

In contiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

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.

contiBAIT documentation built on Nov. 8, 2020, 5:49 p.m.