reorientAndMergeLGs,LinkageGroupList,StrandStateMatrix-method {contiBAIT} | R Documentation |
reorientAndMergeLGs uses a simple dissimilarity to find misoriented fragments within linkage groups.
## S4 method for signature 'LinkageGroupList,StrandStateMatrix' reorientAndMergeLGs(object, allStrands, cluster = NULL, clusterParam = NULL, similarityCutoff = 0.9, verbose = TRUE)
object |
List of vectors containing names of contigs belonging to each LG. |
allStrands |
Table of type |
cluster |
Number of times to recluster and take the consensus of. If NULL, clustering is run only once. |
clusterParam |
optional |
similarityCutoff |
merge contigs that are more similar this this |
verbose |
Outputs information to the terminal. Default is TRUE. |
a list consisting of a strandStateMatrix (a reoriented version of allStrands), a ChrTable containing contig names and orientations, as '+' or '-' and a merged LinkageGroupList.
data(exampleLGList) data(exampleWCMatrix) reorientedMatrix <- reorientAndMergeLGs(exampleLGList, exampleWCMatrix) # Note that in this example data, everything is correctly oreiented to # to begin with, so all contigs come out as + orientation