Man pages for contiBAIT
Improves Early Build Genome Assemblies using Strand-Seq Data
| BAIT | BAIT - master function to process strand-seq libraries into... |
| barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method | Bar plot all linkage groups, with the true chromosomes of... |
| ChrTable | A class for storing chromosome/fragment lengths |
| clusterContigs-StrandStateMatrix-method | clusterContigs - agglomeratively clusters contigs into... |
| contiBAIT | contiBAIT - master function to process strand-seq libraries... |
| ContigOrdering | A class for storing contig ordering of a linkage group |
| exampleChrTable | Example of a ChromosomeTable, containing contigs and their... |
| exampleContigOrder | Example of a ContigOrdering table, containing a list with a... |
| exampleCrickFreq | An example Crick strand frequences extracted from BAMS by... |
| exampleDividedChr | Example of a divided chromosome, containing contigs and their... |
| 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... |
| exampleStrandFreq | Example of strand frequencies extracted from BAMS by... |
| exampleWatsonFreq | An example Watson strand frequences extracted from BAMS by... |
| exampleWCMatrix | An example StrandStateMatrix containing WW, CC and WC calls... |
| findSexGroups-LinkageGroupList-StrandStateMatrix-method | Bar plot all linkage groups, with the true chromosomes of... |
| findSimilarLibraries | findSimilarLibraries - function to identify libraries that... |
| fixLinkageGroups | fixLinkageGroups - searches for discrepancies within ordered... |
| flipOrderedLinkageGroups | flipOrderedLinkageGroups - Simple greedy algorithm to find... |
| highlightAssemblyErrors | highlightAssemblyErrors - Master function to identify... |
| ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method | ideogramPlot - plots BAIT-like ideograms |
| LibraryGroupList | A class for storing library group calls for contigs |
| LinkageGroupList | A class for storing linkage group calls for contigs |
| locateMisorients | locateMisorients - function to identify libraries that hare... |
| makeBoxPlot | makeBoxPlot - creates boxplot of contigs included in the... |
| makeChrTable | makeChrTable - Pulls out chromosome and length data from the... |
| mapGapFromOverlap | mapGapFromOverlap - function to co-localize strand state... |
| mergeFlankedLGs | mergeFlankedLGs - searches for similarities at the ends of... |
| orderAllLinkageGroups | Function to call contig ordering algorithms iteratively... |
| orderContigsGreedy | Function to order contigs within a single linkage group using... |
| orderContigsTSP | Attempt to order contigs within linkage groups using... |
| plotContigOrder | Plot ordering of contigs within a single linkage group. |
| plotLGDistances-LinkageGroupList-StrandStateMatrix-method | plotLGDistances - plots a heatmap of the distances between... |
| plotWCdistribution-StrandFreqMatrix-method | Creates median distribution boxplots across all libraries and... |
| preprocessStrandTable-StrandFreqMatrix-method | preprocessStrandTable - remove low quality libraries and... |
| reorientAndMergeLGs | reorientAndMergeLGs uses a simple dissimilarity to find... |
| 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 |
| StrandFreqMatrix | A class for storing a matrix of frequencies of Watson to... |
| StrandReadMatrix | A class for storing read counts for a set of contigs over... |
| strandSeqFreqTable | strandSeqFreqTable - function to process bam files for... |
| StrandStateList | A class for storing StrandStateList lists for contigs |
| StrandStateMatrix | A class for storing a data frame of discrete strand states of... |
| thoroughBed | thoroughBed - function to merge chromosomes from libraries... |
| writeBed | function to write contig order to BED file |
