mergeFlankedLGs,LinkageGroupList,StrandStateMatrix-method {contiBAIT} | R Documentation |
mergeFlankedLGs – searches for similarities at the ends of ordered linkage groups to chain groups together
## S4 method for signature 'LinkageGroupList,StrandStateMatrix' mergeFlankedLGs(linkageGroupList, strandStateMatrix, buildConsensus = 1, cluster = NULL, clusterParam = NULL, similarityCutoff = 0.7, verbose = TRUE)
linkageGroupList |
List of ordered vectors containing names of contigs belonging to each LG, of type LinkageGroupList |
strandStateMatrix |
Table of type strandStateMatrix encompassing strand state for all contigs. Product of StrandSeqFreqTable. |
buildConsensus |
number of contigs to take at the end of the linkage group to build a consensus strand state. Default is 5 |
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 containing a revised LinkageGroupList with merged groups, if appropriate, and a StrandStateMatrix with contigs reoriented, if newly merged groups were in opposite orientations.