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
