Improves Early Build Genome Assemblies using Strand-Seq Data


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Documentation for package ‘contiBAIT’ version 1.2.0

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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
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.
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
OrientationFrame A class for storing contig orientations
OrientationFrame-class A class for storing contig orientations
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
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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-method function to write contig order to BED file
writeBed-OrientationFrame-ContigOrdering-method function to write contig order to BED file