inst/examples/orderAllLinkageGroups.R

In contiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

#Get a data.frame of ordered contigs from cells from the same organism, aligned to the same genome
 
data("exampleLGList")
data("exampleWCMatrix")
data("exampleStrandFreq")
data("exampleReadCounts")
contigOrder <- orderAllLinkageGroups(exampleLGList, exampleWCMatrix, exampleStrandFreq, exampleReadCounts)

show(contigOrder)

contigOrder <- orderAllLinkageGroups(exampleLGList, exampleWCMatrix, exampleStrandFreq, exampleReadCounts, orderCall='TSP')
show(contigOrder)