fixLinkageGroups,ContigOrdering,StrandStateList,LinkageGroupList-method {contiBAIT} | R Documentation |
fixLinkageGroups – searches for discrepancies within ordered contigs to highlight erroneously merged fragments.
## S4 method for signature 'ContigOrdering,StrandStateList,LinkageGroupList' fixLinkageGroups(contigOrdering, orderFrame, linkageGroupList, whichLG = NULL, relatedCutOff = 0.6, verbose = TRUE)
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. |
a LinkageGroupList with erroneously clustered contigs seperated into their own groups