├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R ├── CCcolors-data.R ├── RcppExports.R ├── add_threshold.R ├── align_scan1_map.R ├── arg_util.R ├── assign_allele_codes.R ├── batch_cols.R ├── batch_vec.R ├── bayes_int.R ├── calc_entropy.R ├── calc_errorlod.R ├── calc_geno_freq.R ├── calc_genoprob.R ├── calc_genoprob2.R ├── calc_grid.R ├── calc_het.R ├── calc_kinship.R ├── calc_raw_summaries.R ├── calc_sdp.R ├── cbind_calc_genoprob.R ├── cbind_expand.R ├── cbind_scan1.R ├── cbind_sim_geno.R ├── cbind_viterbi.R ├── check_cross2.R ├── chisq_colpairs.R ├── chr_lengths.R ├── clean.R ├── clean_genoprob.R ├── clean_scan1.R ├── cluster_util.R ├── compare_geno.R ├── compare_genoprob.R ├── compare_maps.R ├── convert2cross2.R ├── count_xo.R ├── covariates.R ├── create_gene_query_func.R ├── create_marker_index.R ├── create_snpinfo.R ├── create_variant_query_func.R ├── decomp_kinship.R ├── dim_calc_genoprob.R ├── drop_markers.R ├── est_herit.R ├── est_map.R ├── find_common_ids.R ├── find_dup_markers.R ├── find_ibd_segments.R ├── find_index_snp.R ├── find_map_gaps.R ├── find_marker.R ├── find_markerpos.R ├── find_peaks.R ├── find_peaks_and_bayesint.R ├── find_peaks_and_lodint.R ├── fit1.R ├── fit1_pg.R ├── fread_csv.R ├── fread_csv_numer.R ├── genoprob_col2drop.R ├── genoprob_to_alleleprob.R ├── genoprob_to_snpprob.R ├── get_common_ids.R ├── get_x_covar.R ├── guess_phase.R ├── hmm_util.R ├── index_snps.R ├── insert_pseudomarkers.R ├── interp_genoprob.R ├── interp_map.R ├── is_phase_known.R ├── is_same.R ├── kinship_util.R ├── locate_xo.R ├── lod_int.R ├── map_functions.R ├── map_to_grid.R ├── mat2strata.R ├── max_scan1.R ├── maxmarg.R ├── myround.R ├── n_missing.R ├── plot_coef.R ├── plot_coef_and_lod.R ├── plot_genes.R ├── plot_genoprob.R ├── plot_genoprobcomp.R ├── plot_lodpeaks.R ├── plot_onegeno.R ├── plot_peaks.R ├── plot_pxg.R ├── plot_scan1.R ├── plot_sdp.R ├── plot_snpasso.R ├── plot_snpasso_and_genes.R ├── plot_snpasso_and_sdp.R ├── plot_snpasso_sdp_and_genes.R ├── predict_snpgeno.R ├── probs_to_grid.R ├── pull_genoprobint.R ├── pull_genoprobpos.R ├── qtl2-internal.R ├── qtl2-package.R ├── qtl2version.R ├── rbind_calc_genoprob.R ├── rbind_scan1.R ├── rbind_sim_geno.R ├── rbind_viterbi.R ├── rcbind_scan1perm.R ├── read_cross2.R ├── read_pheno.R ├── recode_snps.R ├── reduce_map_gaps.R ├── reduce_markers.R ├── reduce_to_index_snps.R ├── replace_ids.R ├── scale_kinship.R ├── scan1.R ├── scan1_binary.R ├── scan1_pg.R ├── scan1blup.R ├── scan1blup_pg.R ├── scan1coef.R ├── scan1coef_pg.R ├── scan1max.R ├── scan1max_pg.R ├── scan1perm.R ├── scan1perm_pg.R ├── scan1snps.R ├── sim_geno.R ├── sim_geno2.R ├── smooth_gmap.R ├── snpprob_from_cross.R ├── subset_calc_genoprob.R ├── subset_chr.R ├── subset_cross2.R ├── subset_ind.R ├── subset_kinship.R ├── subset_scan1.R ├── subset_sim_geno.R ├── subset_viterbi.R ├── summary_cross2.R ├── summary_scan1perm.R ├── swap_colname.R ├── test_util.R ├── top_snps.R ├── unsmooth_gmap.R ├── viridis.R ├── viterbi.R ├── viterbi2.R ├── weights_util.R ├── write_control_file.R ├── xpos_scan1.R └── zip_datafiles.R ├── README.md ├── data ├── CCaltcolors.RData ├── CCcolors.RData └── CCorigcolors.RData ├── inst ├── CITATION ├── extdata │ ├── ReadMe.md │ ├── cc_variants_small.sqlite │ ├── grav2.zip │ ├── iron.zip │ └── mouse_genes_small.sqlite └── scripts │ ├── .gitignore │ ├── ReadMe.md │ ├── create_ccvariants.R │ ├── create_ccvariants_small.R │ ├── create_mousegenes.R │ ├── create_mousegenes_mgi.R │ └── create_mousegenes_small.R ├── man ├── CCcolors.Rd ├── add_threshold.Rd ├── basic_summaries.Rd ├── batch_cols.Rd ├── batch_vec.Rd ├── bayes_int.Rd ├── calc_entropy.Rd ├── calc_errorlod.Rd ├── calc_geno_freq.Rd ├── calc_genoprob.Rd ├── calc_grid.Rd ├── calc_het.Rd ├── calc_kinship.Rd ├── calc_raw_founder_maf.Rd ├── calc_raw_geno_freq.Rd ├── calc_raw_het.Rd ├── calc_raw_maf.Rd ├── calc_sdp.Rd ├── cbind.calc_genoprob.Rd ├── cbind.scan1.Rd ├── cbind.scan1perm.Rd ├── cbind.sim_geno.Rd ├── cbind.viterbi.Rd ├── cbind_expand.Rd ├── check_cross2.Rd ├── chisq_colpairs.Rd ├── chr_lengths.Rd ├── clean.Rd ├── clean_genoprob.Rd ├── clean_scan1.Rd ├── compare_founder_geno.Rd ├── compare_geno.Rd ├── compare_genoprob.Rd ├── compare_maps.Rd ├── convert2cross2.Rd ├── count_xo.Rd ├── create_gene_query_func.Rd ├── create_snpinfo.Rd ├── create_variant_query_func.Rd ├── decomp_kinship.Rd ├── drop_markers.Rd ├── drop_nullmarkers.Rd ├── est_herit.Rd ├── est_map.Rd ├── find_dup_markers.Rd ├── find_ibd_segments.Rd ├── find_index_snp.Rd ├── find_map_gaps.Rd ├── find_marker.Rd ├── find_markerpos.Rd ├── find_peaks.Rd ├── fit1.Rd ├── fread_csv.Rd ├── fread_csv_numer.Rd ├── genoprob_to_alleleprob.Rd ├── genoprob_to_snpprob.Rd ├── get_common_ids.Rd ├── get_x_covar.Rd ├── guess_phase.Rd ├── index_snps.Rd ├── insert_pseudomarkers.Rd ├── interp_genoprob.Rd ├── interp_map.Rd ├── invert_sdp.Rd ├── locate_xo.Rd ├── lod_int.Rd ├── map_to_grid.Rd ├── mat2strata.Rd ├── max_compare_geno.Rd ├── max_scan1.Rd ├── maxlod.Rd ├── maxmarg.Rd ├── n_missing.Rd ├── plot_coef.Rd ├── plot_compare_geno.Rd ├── plot_genes.Rd ├── plot_genoprob.Rd ├── plot_genoprobcomp.Rd ├── plot_lodpeaks.Rd ├── plot_onegeno.Rd ├── plot_peaks.Rd ├── plot_pxg.Rd ├── plot_scan1.Rd ├── plot_sdp.Rd ├── plot_snpasso.Rd ├── predict_snpgeno.Rd ├── print.cross2.Rd ├── print.summary.scan1perm.Rd ├── probs_to_grid.Rd ├── pull_genoprobint.Rd ├── pull_genoprobpos.Rd ├── pull_markers.Rd ├── qtl2-internal.Rd ├── qtl2-package.Rd ├── qtl2version.Rd ├── rbind.calc_genoprob.Rd ├── rbind.scan1.Rd ├── rbind.scan1perm.Rd ├── rbind.sim_geno.Rd ├── rbind.viterbi.Rd ├── read_cross2.Rd ├── read_pheno.Rd ├── recode_snps.Rd ├── reduce_map_gaps.Rd ├── reduce_markers.Rd ├── replace_ids.Rd ├── scale_kinship.Rd ├── scan1.Rd ├── scan1blup.Rd ├── scan1coef.Rd ├── scan1max.Rd ├── scan1perm.Rd ├── scan1snps.Rd ├── sdp2char.Rd ├── sim_geno.Rd ├── smooth_gmap.Rd ├── subset.calc_genoprob.Rd ├── subset.cross2.Rd ├── subset.sim_geno.Rd ├── subset.viterbi.Rd ├── subset_scan1.Rd ├── summary.cross2.Rd ├── summary_compare_geno.Rd ├── summary_scan1perm.Rd ├── top_snps.Rd ├── unsmooth_gmap.Rd ├── viterbi.Rd ├── write_control_file.Rd ├── xpos_scan1.Rd └── zip_datafiles.Rd ├── src ├── RcppExports.cpp ├── arrange_genes.cpp ├── arrange_genes.h ├── bayes_int.cpp ├── bayes_int.h ├── binreg.cpp ├── binreg.h ├── binreg_eigen.cpp ├── binreg_eigen.h ├── binreg_weighted.cpp ├── binreg_weighted.h ├── binreg_weighted_eigen.cpp ├── binreg_weighted_eigen.h ├── brent_fmin.cpp ├── brent_fmin.h ├── calc_kinship.cpp ├── calc_kinship.h ├── check_cross.cpp ├── check_cross.h ├── chisq_colpairs.cpp ├── chisq_colpairs.h ├── clean_genoprob.cpp ├── clean_genoprob.h ├── compare_geno.cpp ├── compare_geno.h ├── count_xo.cpp ├── count_xo.h ├── cross.cpp ├── cross.h ├── cross_ail.cpp ├── cross_ail.h ├── cross_ail3.cpp ├── cross_ail3.h ├── cross_ail3pk.cpp ├── cross_ail3pk.h ├── cross_ailpk.cpp ├── cross_ailpk.h ├── cross_bc.cpp ├── cross_bc.h ├── cross_dh.h ├── cross_dh6.cpp ├── cross_dh6.h ├── cross_do.cpp ├── cross_do.h ├── cross_do_util.cpp ├── cross_do_util.h ├── cross_dof1.cpp ├── cross_dof1.h ├── cross_dopk.cpp ├── cross_dopk.h ├── cross_f2.cpp ├── cross_f2.h ├── cross_f2pk.cpp ├── cross_f2pk.h ├── cross_genail.cpp ├── cross_genail.h ├── cross_genril.cpp ├── cross_genril.h ├── cross_haploid.cpp ├── cross_haploid.h ├── cross_hs.cpp ├── cross_hs.h ├── cross_hsf1.cpp ├── cross_hsf1.h ├── cross_hspk.cpp ├── cross_hspk.h ├── cross_magic19.cpp ├── cross_magic19.h ├── cross_riself.cpp ├── cross_riself.h ├── cross_riself16.cpp ├── cross_riself16.h ├── cross_riself4.cpp ├── cross_riself4.h ├── cross_riself8.cpp ├── cross_riself8.h ├── cross_risib.cpp ├── cross_risib.h ├── cross_risib4.cpp ├── cross_risib4.h ├── cross_risib8.cpp ├── cross_risib8.h ├── cross_util.cpp ├── cross_util.h ├── debug_util.cpp ├── debug_util.h ├── find_dup_markers.cpp ├── find_dup_markers.h ├── find_ibd_segments.cpp ├── find_ibd_segments.h ├── find_peaks.cpp ├── find_peaks.h ├── fit1_binary.cpp ├── fit1_binary.h ├── fit1_hk.cpp ├── fit1_hk.h ├── fit1_pg.cpp ├── fit1_pg.h ├── geno_names.cpp ├── geno_names.h ├── genoprob_to_alleleprob.cpp ├── genoprob_to_alleleprob.h ├── get_x_covar.cpp ├── get_x_covar.h ├── guess_phase.cpp ├── guess_phase.h ├── hmm_calcerrorlod.cpp ├── hmm_calcerrorlod.h ├── hmm_calcgenoprob.cpp ├── hmm_calcgenoprob.h ├── hmm_calcgenoprob2.cpp ├── hmm_calcgenoprob2.h ├── hmm_estmap.cpp ├── hmm_estmap.h ├── hmm_estmap2.cpp ├── hmm_estmap2.h ├── hmm_forwback.cpp ├── hmm_forwback.h ├── hmm_forwback2.cpp ├── hmm_forwback2.h ├── hmm_simgeno.cpp ├── hmm_simgeno.h ├── hmm_simgeno2.cpp ├── hmm_simgeno2.h ├── hmm_util.cpp ├── hmm_util.h ├── hmm_viterbi.cpp ├── hmm_viterbi.h ├── hmm_viterbi2.cpp ├── hmm_viterbi2.h ├── interp_genoprob.cpp ├── interp_genoprob.h ├── interpolate_maps.cpp ├── interpolate_maps.h ├── linreg.cpp ├── linreg.h ├── linreg_eigen.cpp ├── linreg_eigen.h ├── lmm.cpp ├── lmm.h ├── locate_xo.cpp ├── locate_xo.h ├── lod_int.cpp ├── lod_int.h ├── matrix.cpp ├── matrix.h ├── maxmarg.cpp ├── maxmarg.h ├── predict_snpgeno.cpp ├── predict_snpgeno.h ├── r_message.cpp ├── r_message.h ├── random.cpp ├── random.h ├── reduce_markers.cpp ├── reduce_markers.h ├── scan1_binary.cpp ├── scan1_binary.h ├── scan1_hk.cpp ├── scan1_hk.h ├── scan1_pg.cpp ├── scan1_pg.h ├── scan1blup.cpp ├── scan1blup.h ├── scan1coef_binary.cpp ├── scan1coef_binary.h ├── scan1coef_hk.cpp ├── scan1coef_hk.h ├── scan1coef_pg.cpp ├── scan1coef_pg.h ├── snpprobs.cpp ├── snpprobs.h ├── test_hmm.cpp └── test_hmm.h └── tests ├── testthat.R └── testthat ├── _snaps ├── plot_coef │ └── plot-coef.svg ├── plot_genes │ └── plot-genes.svg ├── plot_genoprob │ └── plot-genoprob.svg ├── plot_peaks │ ├── plot-peaks-noci.svg │ └── plot-peaks.svg ├── plot_pxg │ ├── plot-pxg-se.svg │ └── plot-pxg.svg ├── plot_scan1 │ ├── plot-scan1-onechr.svg │ └── plot-scan1.svg └── plot_sdp │ └── plot-sdp.svg ├── helper-utils.R ├── test-addlog.R ├── test-align_scan1_map.R ├── test-arrange_genes.R ├── test-assign_allele_codes.R ├── test-basic_summaries.R ├── test-batch_cols.R ├── test-binreg.R ├── test-calc_entropy.R ├── test-calc_geno_freq.R ├── test-calc_grid.R ├── test-calc_het.R ├── test-calc_kinship.R ├── test-calc_raw_summaries.R ├── test-calc_sdp.R ├── test-calcerrorlod.R ├── test-calcgenoprob.R ├── test-calcgenoprob2.R ├── test-cbind_expand.R ├── test-check_cross.R ├── test-chisq_colpairs.R ├── test-chr_lengths.R ├── test-clean_genoprob.R ├── test-clean_scan1.R ├── test-compare_founder_geno.R ├── test-compare_geno.R ├── test-compare_maps.R ├── test-control_files.R ├── test-convert2cross2.R ├── test-count_xo.R ├── test-create_gene_query_func.R ├── test-create_marker_index.R ├── test-create_snpinfo.R ├── test-create_variant_query_func.R ├── test-cross_util.R ├── test-crossinfo_sex.R ├── test-decomp_kinship.R ├── test-drop_depcols.R ├── test-drop_markers.R ├── test-est_herit.R ├── test-estmap.R ├── test-estmap2.R ├── test-expand_snp_results.R ├── test-find_common_ids.R ├── test-find_dup_markers.R ├── test-find_ibd_segments.R ├── test-find_index_snp.R ├── test-find_map_gaps.R ├── test-find_marker.R ├── test-find_peaks.R ├── test-fit1.R ├── test-fit1_binary.R ├── test-force_intcovar.R ├── test-genoprob_to_alleleprob.R ├── test-genoprobs_col2drop.R ├── test-get_common_ids.R ├── test-get_x_covar.R ├── test-guess_phase.R ├── test-hmmbasic-ail.R ├── test-hmmbasic-ail3.R ├── test-hmmbasic-ail3pk.R ├── test-hmmbasic-ailpk.R ├── test-hmmbasic-bc.R ├── test-hmmbasic-dh.R ├── test-hmmbasic-dh6.R ├── test-hmmbasic-do.R ├── test-hmmbasic-dof1.R ├── test-hmmbasic-dopk.R ├── test-hmmbasic-f2.R ├── test-hmmbasic-f2pk.R ├── test-hmmbasic-genail.R ├── test-hmmbasic-genril.R ├── test-hmmbasic-haploid.R ├── test-hmmbasic-hs.R ├── test-hmmbasic-hsf1.R ├── test-hmmbasic-hspk.R ├── test-hmmbasic-magic19.R ├── test-hmmbasic-riself.R ├── test-hmmbasic-riself4-8-16.R ├── test-hmmbasic-risib.R ├── test-hmmbasic-risib4-8.R ├── test-index_snps.R ├── test-interp_genoprob.R ├── test-interpmap.R ├── test-io.R ├── test-is_phase_known.R ├── test-is_same.R ├── test-kinship_util.R ├── test-linreg.R ├── test-lmm.R ├── test-map_to_grid.R ├── test-map_to_pos.R ├── test-mapfunc.R ├── test-mat2strata.R ├── test-matrix.R ├── test-max_scan1.R ├── test-maxmarg.R ├── test-n_missing.R ├── test-plot_coef.R ├── test-plot_genes.R ├── test-plot_genoprob.R ├── test-plot_peaks.R ├── test-plot_pxg.R ├── test-plot_scan1.R ├── test-plot_sdp.R ├── test-predict_snpgeno.R ├── test-probs_to_grid.R ├── test-pseudomarkermap.R ├── test-pull_genoprobint.R ├── test-pull_genoprobpos.R ├── test-rcbind_calcgenoprob.R ├── test-rcbind_scan1.R ├── test-rcbind_scan1perm.R ├── test-rcbind_simgeno.R ├── test-rcbind_viterbi.R ├── test-read_issues.R ├── test-recode_snps.R ├── test-reduce_map_gaps.R ├── test-reduce_markers.R ├── test-reduce_to_indexed_snps.R ├── 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