# Improves Early Build Genome Assemblies using Strand-Seq Data

## Documentation for package ‘contiBAIT’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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