orderAllLinkageGroups,LinkageGroupList,StrandStateMatrix,StrandFreqMatrix,StrandReadMatrix-method {contiBAIT} | R Documentation |
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)