BAIT                    BAIT - master function to process strand-seq
                        libraries into BAIT ideograms
ChrTable-class          A class for storing chromosome/fragment lengths
ContigOrdering-class    A class for storing contig ordering of a
                        linkage group
LibraryGroupList-class
                        A class for storing library group calls for
                        contigs
LinkageGroupList-class
                        A class for storing linkage group calls for
                        contigs
StrandFreqMatrix-class
                        A class for storing a matrix of frequencies of
                        Watson to Crick reads for a set of contigs over
                        several libraries
StrandReadMatrix-class
                        A class for storing read counts for a set of
                        contigs over several libraries
StrandStateList-class   A class for storing StrandStateList lists for
                        contigs
StrandStateMatrix-class
                        A class for storing a data frame of discrete
                        strand states of a set of contigs over several
                        libraries
barplotLinkageGroupCalls,LinkageGroupList,ChrTable-method
                        Bar plot all linkage groups, with the true
                        chromosomes of contigs coloured.
clusterContigs,StrandStateMatrix-method
                        clusterContigs - agglomeratively clusters
                        contigs into linkage groups based on strand
                        inheritance
contiBAIT               contiBAIT - master function to process
                        strand-seq libraries into ordered linkage
                        groups
exampleChrTable         Example of a ChromosomeTable, containing
                        contigs and their lengths
exampleContigOrder      Example of a ContigOrdering table, containing a
                        list with a matrix of ordered groups element
                        and a StrandStateList element
exampleCrickFreq        An example Crick strand frequences extracted
                        from BAMS by strandSeqFreqTable where
                        BAITtables=TRUE
exampleDividedChr       Example of a divided chromosome, containing
                        contigs and their lengths
exampleLGList           Example of a LinkageGroupList output from
                        clusterContigs
exampleLibList          Example of a LibraryGroupList, containing
                        library names
exampleReadCounts       Example of read counts extracted from BAMS by
                        strandSeqFreqTable
exampleStrandFreq       Example of strand frequencies extracted from
                        BAMS by strandSeqFreqTable
exampleWCMatrix         An example StrandStateMatrix containing WW, CC
                        and WC calls for contigs
exampleWatsonFreq       An example Watson strand frequences extracted
                        from BAMS by strandSeqFreqTable where
                        BAITtables=TRUE
findSexGroups,LinkageGroupList,StrandStateMatrix-method
                        Bar plot all linkage groups, with the true
                        chromosomes of contigs coloured.
findSimilarLibraries,StrandStateMatrix,StrandReadMatrix,ChrTable-method
                        findSimilarLibraries - function to identify
                        libraries that hare similar WC patterns on
                        chromosomes
fixLinkageGroups,ContigOrdering,StrandStateList,LinkageGroupList-method
                        fixLinkageGroups - searches for discrepancies
                        within ordered contigs to highlight erroneously
                        merged fragments.
flipOrderedLinkageGroups,ContigOrdering,StrandStateList,LinkageGroupList,StrandStateMatrix-method
                        flipOrderedLinkageGroups - Simple greedy
                        algorithm to find misorientations within
                        previously ordered LG.
highlightAssemblyErrors
                        highlightAssemblyErrors - Master function to
                        identify misorientations and chimeras in the
                        assembly
ideogramPlot,StrandReadMatrix,StrandReadMatrix,ChrTable-method
                        ideogramPlot - plots BAIT-like ideograms
locateMisorients,GRanges-method
                        locateMisorients - function to identify
                        libraries that hare similar WC patterns on
                        chromosomes
makeBoxPlot,ChrTable,LinkageGroupList-method
                        makeBoxPlot - creates boxplot of contigs
                        included in the analysis vs those excluded
makeChrTable            makeChrTable - Pulls out chromosome and length
                        data from the header of a bam file
mapGapFromOverlap       mapGapFromOverlap - function to co-localize
                        strand state changes with assembly gaps
mergeFlankedLGs,LinkageGroupList,StrandStateMatrix-method
                        mergeFlankedLGs - searches for similarities at
                        the ends of ordered linkage groups to chain
                        groups together
orderAllLinkageGroups,LinkageGroupList,StrandStateMatrix,StrandFreqMatrix,StrandReadMatrix-method
                        Function to call contig ordering algorithms
                        iteratively across each linkage group element
orderContigsGreedy      Function to order contigs within a single
                        linkage group using a greedy algorithms Attempt
                        to order contigs within
orderContigsTSP         Attempt to order contigs within linkage groups
                        using travelling salesperson algorithm
plotContigOrder,ContigOrdering-method
                        Plot ordering of contigs within a single
                        linkage group.
plotLGDistances,LinkageGroupList,StrandStateMatrix-method
                        plotLGDistances - plots a heatmap of the
                        distances between linkage groups
plotWCdistribution,StrandFreqMatrix-method
                        Creates median distribution boxplots across all
                        libraries and contigs
preprocessStrandTable,StrandFreqMatrix-method
                        preprocessStrandTable - remove low quality
                        libraries and contigs before attempting to
                        build a genome
reorientAndMergeLGs,LinkageGroupList,StrandStateMatrix-method
                        reorientAndMergeLGs uses a simple dissimilarity
                        to find misoriented fragments within linkage
                        groups.
show,ContigOrdering-method
                        show-methods
show,LibraryGroupList-method
                        show-methods
show,LinkageGroupList-method
                        show-methods
show,OrientationFrame-method
                        show-methods
show,StrandFreqMatrix-method
                        show-methods
show,StrandReadMatrix-method
                        show-methods
show,StrandStateList-method
                        show-methods
show,StrandStateMatrix-method
                        show-methods
strandSeqFreqTable      strandSeqFreqTable - function to process bam
                        files for contiBAIT
thoroughBed,ANY,LibraryGroupList-method
                        thoroughBed - function to merge chromosomes
                        from libraries that have the same strand states
writeBed,ANY,ChrTable,ContigOrdering-method
                        function to write contig order to BED file
