Files in bahlolab/XIBD

Identity-by-Descent Analysis of the Human Genome

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/RcppExports.R R/calculate_allele_freq.R R/colour_palette.R R/condition_snps.R R/data_processing.R R/example_genotypes.R R/example_hapmap_topbot.R R/example_ibd.R R/example_parameters.R R/example_pedmap.R R/example_reference_ld.R R/example_reference_pedmap.R R/ibd_detection.R R/identity_coefficients.R R/identity_coefficients_a.R R/identity_coefficients_x.R R/locus_matrix.R R/locus_proportions.R R/meiosis.R R/merge_lists.R R/parameter_estimates.R R/plot_ibd_segments.R R/plot_locus_proportions.R R/segment_summary.R R/switch_bot_genotypes.R README.md

XIBD.Rproj

data/example_genotypes.rda

data/example_hapmap_topbot.rda

data/example_ibd.rda

data/example_parameters.rda

data/example_pedmap.rda

data/example_reference_ld.rda

data/example_reference_pedmap.rda

docs/LICENSE.html

docs/README.html

docs/articles/index.html

docs/articles/introduction.html

docs/articles/introduction_files/figure-html/unnamed-chunk-2-1.png

docs/articles/introduction_files/figure-html/unnamed-chunk-2-2.png

docs/articles/introduction_files/figure-html/unnamed-chunk-5-1.png

docs/articles/introduction_files/figure-html/unnamed-chunk-6-1.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/calculateAlleleFreq.html

docs/reference/example_genotypes.html

docs/reference/example_hapmap_topbot.html

docs/reference/example_ibd.html

docs/reference/example_parameters.html

docs/reference/example_pedmap.html

docs/reference/example_reference_ld.html

docs/reference/example_reference_pedmap.html

docs/reference/getColourPaletteMajor.html

docs/reference/getColourPaletteMinor.html

docs/reference/getConditionSNP.html

docs/reference/getGenotypes.html

docs/reference/getHaplotypeFreq.html

docs/reference/getIBDparameters.html

docs/reference/getIBDsegments.html

docs/reference/getIdentityCoef.html

docs/reference/getLocusMatrix.html

docs/reference/getLocusProportion.html

docs/reference/index.html

docs/reference/plotIBDproportions-1.png

docs/reference/plotIBDproportions.html

docs/reference/plotIBDsegments-1.png

docs/reference/plotIBDsegments.html

docs/reference/switchBOTgenotypes-1.png

docs/reference/switchBOTgenotypes-2.png

docs/reference/switchBOTgenotypes.html

inst/CITATION

man/calculateAlleleFreq.Rd man/example_genotypes.Rd man/example_hapmap_topbot.Rd man/example_ibd.Rd man/example_parameters.Rd man/example_pedmap.Rd man/example_reference_ld.Rd man/example_reference_pedmap.Rd man/getColourPaletteMajor.Rd man/getColourPaletteMinor.Rd man/getConditionSNP.Rd man/getGenotypes.Rd man/getHaplotypeFreq.Rd man/getIBDparameters.Rd man/getIBDsegments.Rd man/getIdentityCoef.Rd man/getLocusMatrix.Rd man/getLocusProportion.Rd man/plotIBDproportions.Rd man/plotIBDsegments.Rd man/switchBOTgenotypes.Rd

src/RcppExports.cpp

src/binary_ibd_matrix.cpp

src/calculate_missingness.cpp

src/calculate_pop_allele_freq.cpp

src/generate_group_pairs.cpp

src/haplotype_frequencies.cpp

src/haplotypes_to_genotypes.cpp

src/ibd_labels.cpp

src/isolate_pairs.cpp

src/model_1_hmm.cpp

src/model_2_hmm.cpp

src/parameter_estimates.cpp

src/topbot_change.cpp

vignettes/introduction.Rmd

bahlolab/XIBD documentation built on May 11, 2019, 5:24 p.m.