Man pages for bahlolab/isoRelate
Identity-by-Descent Inference of Haploid Recombining Organisms

AmatrixDDThe matrix A in the equation Ax=b for 2 diploid chromosomes
AmatrixHDThe matrix A in the equation Ax=b for 1 haploid and 1 diploid...
AmatrixHHThe matrix A in the equation Ax=b for 2 haploid chromosomes
annotation_genesPlasmodium Falciparum Gene Annotation Dataset
areColorsInternal function
bVectorDDThe vector b in the equation Ax=b for 2 diploid chromosomes
bVectorHDThe vector b in the equation Ax=b for 1 haploid chromosome...
bVectorHHThe vector b in the equation Ax=b for 2 haploid chromosomes
calculateAlphaCalculate alpha
calculateBetaCalculate beta
calculateGammaCalculate gamma
calculateLogLikelihoodCalculate the log-likelihood of the data
calculateMeiosisEstimation of Meiosis
calculateMissingnessCalculate Missingness Proportions
calculatePopAlleleFreqCalculate Allele Frequencies for SNPs from Genotype Data
calculateScaleCalculate scale
calculateViterbiCalculate the Viterbi sequence
clusterSummaryA function that prints summary information of clusters
emissionProbDDThe emission probabilities for 2 diploid chromosomes
emissionProbHDThe emission probabilities for 1 haploid chromosome and 1...
emissionProbHHThe emission probabilities for 2 haploid chromosomes
emissionProbMissingGenoCalculating the emission probability sumation when missing...
genotypeErrorDThe genotyping error probability for 1 diploid chromosome
genotypeErrorHThe genotyping error probability for 1 haploid chromosome
getColourPaletteMajorIsoRelate Colour Palette for groups
getColourPaletteMinor'getColourPaletteMinor()' generates a specified number of...
getGenotypesPre-Analysis Data Processing
getIBDiclustersInterval Cluster Networks
getIBDiRSelection Significance Statistic
getIBDmatrixBinary IBD Matrix
getIBDparametersParameter Estimation
getIBDpclustersGenome Cluster Networks
getIBDposteriorIBD Posterior Probabilities
getIBDproportionProportion of Pairs IBD
getIBDsegmentsIBD Segment Detection
getIBDsummaryIBD Segment Summary
getOverlapfunction to find IBD that overlap interval
groupPairsGroup Combinations for Analysis
haplotypeToGenotypeCall Genotypes from Haplotype Data
highlight_genesPlasmodium Falciparum Gene Highlight Dataset
IBDLabelInternal Function
IBDMatrixBinary Matrix of IBD
IBDparametersIBDparameters() calculates IBD probabilities then estimates...
IBDTableInternal Function
iRfunctionInternal Function
isolatePairsPair Combinations for Analysis
merge_listsInternal Function
my_ibdIBD Segments For The Papua New Guinea Dataset
plotIBDclustersPlot Cluster Networks
plotIBDiRPlot iR Statistics
plotIBDproportionsPlot The Proportion of Pairs IBD
plotIBDsegmentsPlot IBD Segments
png_genotypesFiltered Genotypes For The Papua New Guinea Dataset
png_ibdIBD Segments For The Papua New Guinea Dataset
png_parametersIBD Parameter Estimates For The Papua New Guinea Dataset
png_pedmapPapua New Guinea Plasmodium Falciparum Dataset
roundDecimalRound digits to specified decimal places
transitionProbDDThe transition probabilities for 2 diploid chromosomes
transitionProbHDThe transition probabilities for 1 haploid and 1 diploid...
transitionProbHHThe transition probabilities for 2 haploid chromosomes
trueGenotypesMatrices of all possible genotype combinations between pairs,...
bahlolab/isoRelate documentation built on May 11, 2019, 5:25 p.m.