Package index • GenomicBreaks

Data loading functions

Functions to load data

load_genomic_breaks(): Load pairwise genome alignments

readMAF(): Read a MAF file

readTrainFile(): Extract values from last-train parameter file

Plotting functions

Graphical display of pairwise alignments

bp_heatmap(): Breakpoint Associated Heatmaps

bp_pair_analysis(): Breakpoint Pairwise Comparison using Reference Genome as Coordinate System

feature_coverage(): Feature coverage heatmap

makeOxfordPlots(): Make Oxford Plots

plotApairOfChrs(): Plots a pair of chromosomes from a GBreaks object.

Heatmap Functions

Functions that return a Heatmap object from the heatmaps package.

bp_heatmap(): Breakpoint Associated Heatmaps

bp_pair_analysis(): Breakpoint Pairwise Comparison using Reference Genome as Coordinate System

feature_coverage(): Feature coverage heatmap

genoPlotR functions

Functions related to the genoPlotR package that we use for pair chromosome plots.

gb2comp(): Convert GBreaks object to a comparison object

gb2dna_seg(): Convert GBreaks object to a list of dna_seg objects

gb2xlim(): GBreaks to xlim

gr2dna_seg(): Convert GRanges object to dna_seg format

plotApairOfChrs(): Plots a pair of chromosomes from a GBreaks object.

Distance functions

Various ways to estimate the similarity between two genomes.

F81_distance(): Felsenstein's 1981 Distance

GOC(): Gene Order Conservation

HKY85_distance(): Hasegawa–Kishino–Yano (1985) distance (HKY85)

JC69_distance(): Jukes-Cantor 1969 distance

K80_distance(): Kimura's 2-parameter distance

P_distance() P_error(): Percent difference Distance

T92_distance(): Tamura 1992 distance

TN93_distance(): Tamura–Nei 1993 distance

correlation_index(): Index representing how correlated syntenic regions are

karyotype_index(): Index representing how the karyotype changes between chromosomes of two genomes

logDet_distance(): LogDet (log-determinant) distance

slidingWindow(): Sliding window

strand_randomisation_index(): Index measuring how 'random' the alignment strand has become.

synteny_index(): Index representing how 'syntenic' two genomes are

tau_index(): Tau index

GCequilibrium(): Equilibrium GC fraction (GC*)

GCpressure(): GC pressure

GCproportion(): Proportion of GC in alignment

exampleSubstitutionMatrix: Example Substitution Matrices

gapProportion(): Proportion of gaps in alignment

Colinearity functions

Functions to analyse colinearity and synteny.

GOC(): Gene Order Conservation

bridgeRegions(): Bridge regions

chain_contigs(): Chain contigs in pairwise alignments

coalesce_contigs(): Coalesce Pairwise Alignments

dist2next(): Distances to next ranges

filterColinearRegions(): Filter colinear regions

flagColinearAlignments(): Flag colinear alignments

flagPairs(): Flag successive entries of a GBreaks object

Flags and filters

Functions to flag patterns of alignments and filter them.

flagAll(): Compute all flags

flagColinearAlignments(): Flag colinear alignments

flagDoubleInversions(): Flag double inversions

flagInversions(): Flag inversions

flagLongShort(): Flag long and short arms

flagPairs(): Flag successive entries of a GBreaks object

flagTranslocations(): Flag translocations

filterColinearRegions(): Filter colinear regions

filterDoubleInversions(): Extract central blocks in double inversions

filterInversions(): Extract central blocks in inversions

filterTranslocations(): Extract central blocks in translocations

showInversions(): Show inversions and their flanking blocks.

showTranslocations(): Show translocations and their flanking blocks.

Bioconductor API functions

Functions that provide compatibility with GRanges, etc.

GBreaks-class GBreaks: The GenomicBreaks class

getSeq(): Get genomic sequences

pairwiseAlignment(): Pairwise alignment of genomic ranges

range_GBreaks() range(<GBreaks>): Range method for GBreaks objects

reverse(): Reverse genomic ranges

subsetByOverlaps_GBreaks() subsetByOverlaps(<GBreaks>,<GBreaks>): subsetByOverlaps method for GBreaks objects

Motifier functions

Functions that take GBreaks objects and return them modified.

bridgeRegions(): Bridge regions

coalesce_contigs(): Coalesce Pairwise Alignments

flipInversions(): Flip strand of inversions

forceSeqLengths(): Set sequence lengths if there were none

guessSeqLengths(): Guesstimate seqlevel lengths

keepLongestPair(): Keep the longest pair of features

matchPairs(): Match pairs of sequences

mergeSeqLevels() mergeSeqLevels_to_DF(): Merge seqlevels in a larger one

removeDoubleInversions(): Remove double inversions

removeInversions(): Remove inversions

removeTranslocations(): Remove translocations

reverse(): Reverse genomic ranges

splitSeqLevel(): Split a seqlevel in two pieces

swap(): Swap target and query genomes

Reducing functions

Functions that take GBreaks objects and return simpler GRanges objects.

cleanGaps(): Gaps between ranges

get_bps(): Get breakpoints

wholeGenomeClassification(): Whole-genome classification object

Converter functions

GBreaksToMatrix(): Convert to binned matrix of hits

gb2comp(): Convert GBreaks object to a comparison object

gb2dna_seg(): Convert GBreaks object to a list of dna_seg objects

gb2xlim(): GBreaks to xlim

gr2dna_seg(): Convert GRanges object to dna_seg format

Scaffolding functions

Functions to aid trivial scaffolding

flipStrandNames(): Reverse order and flip strand

longestMatchesInTarget(): Find longest matches from target to query genome.

mergeSeqLevels() mergeSeqLevels_to_DF(): Merge seqlevels in a larger one

scaffoldByFlipAndMerge(): Guided scaffolding

splitSeqLevel(): Split a seqlevel in two pieces

strandNames(): Sequence name with strand information

Other functions

StructuralVariants exampleColinear exampleNotColinear exampleColinear3 exampleColinear5 exampleInversion exampleNestedInversions exampleInversion5uncollapsed exampleDoubleInversion1 exampleDoubleInversion2 exampleDoubleInversion3 exampleDoubleInversion4 exampleTranslocation exampleTranslocation2 exampleInsertion exampleDeletion: Structural Variants

align_scaf_plot_2(): Compare Alignments over two Reference scaffolds

feature_coverage(): Feature coverage heatmap

int_frag(): Integrated intersection of both query and reference subsets on a continuous alignment

inv2UCSCData(): Represent inversions as UCSCData objects

isSorted(): Test if a GBreaks object is sorted

leftInversionGaps(): Isolate the left-side gaps in inversions

makeInversion.chr(): Make an inversion

orderQuerySeqLevels() orderQuerySeqLevels_DF_GR(): Ordering permutation for query relative to target

scaf_align_plot(): Plot Alignment of Single Reference Scaffold

tan_bp(): Breakpoint proximity to Tandem Repeats

zipWithNext(): Zip elements with the next ones

inversionDistance(): Inversion Distance

permutationVector(): Permutation vector