contiBAIT (version 1.0.0)

orderAllLinkageGroups,LinkageGroupList,StrandStateMatrix,StrandFreqMatrix,StrandReadMatrix-method: Function to call contig ordering algorithms iteratively across each linkage group element

Description

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

Usage

## S3 method for class 'LinkageGroupList,StrandStateMatrix,StrandFreqMatrix,StrandReadMatrix':
orderAllLinkageGroups(linkageGroupList,
  strandStateMatrix, strandFreqMatrix, strandReadCount, whichLG = NULL,
  saveOrdered = FALSE, orderCall = "greedy", randomAttempts = 75,
  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

iterger specifying number of randomized clusterings to identify the best ordering. Default is 75

verbose

Pringts messages to the terminal. Default is TRUE

Value

• a data.frame of ordered contigs with linkage group names

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)