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 |
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-method | function to write contig order to BED file |
writeBed-OrientationFrame-ContigOrdering-method | function to write contig order to BED file |