orderAllLinkageGroups: Function to call contig ordering algorithms iteratively...

In oneillkza/ContiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

Description

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

Usage

  ## 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)

Arguments

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

Value

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.

Examples

#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)

oneillkza/ContiBAIT documentation built on June 1, 2020, 5:49 a.m.