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

Description Usage Arguments Value

Description

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

Usage

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  ## 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


oneillkza/ContiBAIT documentation built on June 1, 2020, 5:49 a.m.