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

Description Usage Arguments Value

Description

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

Usage

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  ## 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


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