flipOrderedLinkageGroups,ContigOrdering,StrandStateList,LinkageGroupList,StrandStateMatrix-method {contiBAIT} | R Documentation

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

### 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

[Package contiBAIT version 1.16.0 Index]