orderAllLinkageGroups: Function to call contig ordering algorithms iteratively...
In contiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

Description Usage Arguments Value Examples

Function to call contig ordering algorithms iteratively across each linkage group element

  ## S4 method for signature 
## 'LinkageGroupList,StrandStateMatrix,StrandFreqMatrix,StrandReadMatrix'
orderAllLinkageGroups(linkageGroupList,
  strandStateMatrix, strandFreqMatrix, strandReadCount, whichLG = NULL,
  saveOrdered = NULL, orderCall = "greedy", randomAttempts = 75,
  nProcesses = 1, verbose = TRUE)

`linkageGroupList`	list of vectors, each specifying which contigs belong in which linkage group (product of clusterContigs)
`strandStateMatrix`	table of strand calls for all contigs (product of preprocessStrandTable)
`strandFreqMatrix`	table of W:C read proportions (used for QC) (product of strandSeqFreqTable[[1]])
`strandReadCount`	table of read counts (product of strandSeqFreqTable[[2]])
`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.
`saveOrdered`	Will return a pdf of heatmaps for each linkage group; String entered becomes the fileName (default is saveOrderedPDF=FALSE)
`orderCall`	currently either 'greedy' for greedy algorithm or 'TSP' for travelling salesperson alogrithm (default is 'greedy')
`randomAttempts`	itenger specifying number of iterations of either the Monte Carlo or the 2-opt TSP solver to identify the best ordering. Default is 75, but higher values (eg 1000) make more sense for the TSP.
`nProcesses`	number of processes to attempt ordering in parallel
`verbose`	Pringts messages to the terminal. Default is TRUE

a list containing a ContigOrdering object consisting of ordered contigs with linkage group names, a StrandStateList consisting of StrandStateMatrices for each LG, and a LinkageGroupList consisting of reordered contigs within each list element.

#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)