flipOrderedLinkageGroups,ContigOrdering,StrandStateList,LinkageGroupList,StrandStateMatrix-method {contiBAIT} | R Documentation |
flipOrderedLinkageGroups – Simple greedy algorithm to find misorientations within previously ordered LG.
## S4 method for signature ## 'ContigOrdering,StrandStateList,LinkageGroupList,StrandStateMatrix' flipOrderedLinkageGroups(contigOrdering, orderFrame, linkageGroupList, strandStateMatrix, whichLG = NULL, maxiter = 100, dissimilarityCutoff = 0.3)
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. |
a StrandStateMatrix with misorientations resolved