fixLinkageGroups: fixLinkageGroups - searches for discrepancies within ordered...

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

Description

fixLinkageGroups – searches for discrepancies within ordered contigs to highlight erroneously merged fragments.

Usage

  ## S4 method for signature 'ContigOrdering,StrandStateList,LinkageGroupList'
fixLinkageGroups(contigOrdering,
  orderFrame, linkageGroupList, whichLG = NULL, relatedCutOff = 0.6,
  verbose = TRUE)

Arguments

contigOrdering	a data.frame of ordered contigs with linkage group names of class ContigOrdering
orderFrame	a list of StrandStateMatrix elements of class StrandStateList
linkageGroupList	List of vectors containing names of contigs belonging to each LG of type LinkageGroupList.
whichLG	vector of integers specifying the element(s) of linkageGroupList to be ordered (i.e. which specific linkage groups to try to order). Default is all LGs.
relatedCutOff	The minimal dissimilarity between adjacent contigs to subset a linkage group into multiple smaller groups. Default is 0.6
verbose	Outputs information to the terminal. Default is TRUE.

Value

a LinkageGroupList with erroneously clustered contigs seperated into their own groups

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