Files in bahlolab/isoRelate

Identity-by-Descent Inference of Haploid Recombining Organisms

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DESCRIPTION

LICENSE

NAMESPACE

R/RcppExports.R R/annotation_genes.R R/data_processing.R R/get_ibd_iR.R R/get_ibd_i_clusters.R R/get_ibd_matrix.R R/get_ibd_p_clusters.R R/get_ibd_parameters.R R/get_ibd_posterior.R R/get_ibd_proportions.R R/get_ibd_segments.R R/get_ibd_summary.R R/highlight_genes.R R/internal_are_colours.R R/internal_colour_palette.R R/internal_get_overlap.R R/internal_iR_function.R R/internal_meiosis.R R/internal_merge_lists.R R/internal_segment_summary.R R/my_ibd.R R/plot_ibd_clusters.R R/plot_ibd_iR.R R/plot_ibd_proportions.R R/plot_ibd_segments.R R/png_genotypes.R R/png_ibd.R R/png_parameters.R R/png_pedmap.R README.md

data/annotation_genes.rda

data/highlight_genes.rda

data/my_ibd.rda

data/png_genotypes.rda

data/png_ibd.rda

data/png_parameters.rda

data/png_pedmap.rda

docs/LICENSE.html

docs/README.html

docs/articles/index.html

docs/articles/introduction.html

docs/articles/introduction_files/figure-html/unnamed-chunk-10-1.png

docs/articles/introduction_files/figure-html/unnamed-chunk-11-1.png

docs/articles/introduction_files/figure-html/unnamed-chunk-12-1.png

docs/articles/introduction_files/figure-html/unnamed-chunk-13-1.png

docs/articles/introduction_files/figure-html/unnamed-chunk-14-1.png

docs/articles/introduction_files/figure-html/unnamed-chunk-15-1.png

docs/articles/introduction_files/figure-html/unnamed-chunk-9-1.png

docs/authors.html

docs/index.html

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/AmatrixDD.html

docs/reference/AmatrixHD.html

docs/reference/AmatrixHH.html

docs/reference/IBDLabel.html

docs/reference/IBDMatrix.html

docs/reference/IBDTable.html

docs/reference/IBDparameters.html

docs/reference/annotation_genes.html

docs/reference/areColors.html

docs/reference/bVectorDD.html

docs/reference/bVectorHD.html

docs/reference/bVectorHH.html

docs/reference/calculateAlpha.html

docs/reference/calculateBeta.html

docs/reference/calculateGamma.html

docs/reference/calculateLogLikelihood.html

docs/reference/calculateMeiosis.html

docs/reference/calculateMissingness.html

docs/reference/calculatePopAlleleFreq.html

docs/reference/calculateScale.html

docs/reference/calculateViterbi.html

docs/reference/clusterSummary.html

docs/reference/emissionProbDD.html

docs/reference/emissionProbHD.html

docs/reference/emissionProbHH.html

docs/reference/emissionProbMissingGeno.html

docs/reference/genotypeErrorD.html

docs/reference/genotypeErrorH.html

docs/reference/getColourPaletteMajor.html

docs/reference/getColourPaletteMinor.html

docs/reference/getGenotypes.html

docs/reference/getIBDiR.html

docs/reference/getIBDiclusters.html

docs/reference/getIBDmatrix.html

docs/reference/getIBDparameters.html

docs/reference/getIBDpclusters.html

docs/reference/getIBDposterior.html

docs/reference/getIBDproportion.html

docs/reference/getIBDsegments.html

docs/reference/getIBDsummary.html

docs/reference/getOverlap.html

docs/reference/groupPairs.html

docs/reference/haplotypeToGenotype.html

docs/reference/highlight_genes.html

docs/reference/iRfunction.html

docs/reference/index.html

docs/reference/isolatePairs.html

docs/reference/merge_lists.html

docs/reference/my_ibd.html

docs/reference/plotIBDclusters-1.png

docs/reference/plotIBDclusters-2.png

docs/reference/plotIBDclusters.html

docs/reference/plotIBDiR-1.png

docs/reference/plotIBDiR.html

docs/reference/plotIBDproportions-1.png

docs/reference/plotIBDproportions-2.png

docs/reference/plotIBDproportions.html

docs/reference/plotIBDsegments-1.png

docs/reference/plotIBDsegments-2.png

docs/reference/plotIBDsegments.html

docs/reference/png_genotypes.html

docs/reference/png_ibd.html

docs/reference/png_parameters.html

docs/reference/png_pedmap.html

docs/reference/roundDecimal.html

docs/reference/transitionProbDD.html

docs/reference/transitionProbHD.html

docs/reference/transitionProbHH.html

docs/reference/trueGenotypes.html

inst/CITATION

isoRelate.Rproj

man/AmatrixDD.Rd man/AmatrixHD.Rd man/AmatrixHH.Rd man/IBDLabel.Rd man/IBDMatrix.Rd man/IBDTable.Rd man/IBDparameters.Rd man/annotation_genes.Rd man/areColors.Rd man/bVectorDD.Rd man/bVectorHD.Rd man/bVectorHH.Rd man/calculateAlpha.Rd man/calculateBeta.Rd man/calculateGamma.Rd man/calculateLogLikelihood.Rd man/calculateMeiosis.Rd man/calculateMissingness.Rd man/calculatePopAlleleFreq.Rd man/calculateScale.Rd man/calculateViterbi.Rd man/clusterSummary.Rd man/emissionProbDD.Rd man/emissionProbHD.Rd man/emissionProbHH.Rd man/emissionProbMissingGeno.Rd man/genotypeErrorD.Rd man/genotypeErrorH.Rd man/getColourPaletteMajor.Rd man/getColourPaletteMinor.Rd man/getGenotypes.Rd man/getIBDiR.Rd man/getIBDiclusters.Rd man/getIBDmatrix.Rd man/getIBDparameters.Rd man/getIBDpclusters.Rd man/getIBDposterior.Rd man/getIBDproportion.Rd man/getIBDsegments.Rd man/getIBDsummary.Rd man/getOverlap.Rd man/groupPairs.Rd man/haplotypeToGenotype.Rd man/highlight_genes.Rd man/iRfunction.Rd man/isolatePairs.Rd man/merge_lists.Rd man/my_ibd.Rd man/plotIBDclusters.Rd man/plotIBDiR.Rd man/plotIBDproportions.Rd man/plotIBDsegments.Rd man/png_genotypes.Rd man/png_ibd.Rd man/png_parameters.Rd man/png_pedmap.Rd man/roundDecimal.Rd man/transitionProbDD.Rd man/transitionProbHD.Rd man/transitionProbHH.Rd man/trueGenotypes.Rd

src/RcppExports.cpp

src/between_hmm.cpp

src/between_parameter_estimates.cpp

src/binary_ibd_matrix.cpp

src/calculate_allele_frequencies.cpp

src/calculate_missingness.cpp

src/generate_group_pairs.cpp

src/generate_isolate_pairs.cpp

src/haplotypes_to_genotypes.cpp

src/ibd_label.cpp

src/symbols.rds

vignettes/introduction.Rmd

bahlolab/isoRelate documentation built on May 11, 2019, 5:25 p.m.