flipOrderedLinkageGroups: flipOrderedLinkageGroups - Simple greedy algorithm to find...

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

Description

flipOrderedLinkageGroups – Simple greedy algorithm to find misorientations within previously ordered LG.

Usage

  ## S4 method for signature 
## 'ContigOrdering,StrandStateList,LinkageGroupList,StrandStateMatrix'
flipOrderedLinkageGroups(contigOrdering,
  orderFrame, linkageGroupList, strandStateMatrix, whichLG = NULL,
  maxiter = 100, dissimilarityCutoff = 0.3)

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. Should be ordered as the output of orderAllLinkageGroups[[3]]
strandStateMatrix	a StrandStateMatrix to be reoriented
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.
maxiter	The number of iterations used to find the optimal path. Default is 100
dissimilarityCutoff	The minimum amount of dissimilarity needed to start reorienting contigs. Default is 0.3.

Value

a StrandStateMatrix with misorientations resolved

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