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