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

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

### 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

[Package contiBAIT version 1.8.0 Index]