Files in qtl2

Quantitative Trait Locus Mapping in Experimental Crosses

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

R/RcppExports.R R/lod_int.R R/get_x_covar.R R/clean_genoprob.R R/summary_scan1perm.R R/plot_pxg.R R/find_marker.R R/scan1max_pg.R R/interp_genoprob.R R/plot_peaks.R R/viridis.R R/calc_geno_freq.R R/scan1blup.R R/rcbind_scan1perm.R R/viterbi2.R R/unsmooth_gmap.R R/create_marker_index.R R/calc_grid.R R/rbind_viterbi.R R/compare_maps.R R/swap_colname.R R/n_missing.R R/genoprob_col2drop.R R/find_peaks_and_bayesint.R R/calc_entropy.R R/create_snpinfo.R R/subset_kinship.R R/sim_geno2.R R/count_xo.R R/scan1coef.R R/pull_genoprobpos.R R/create_variant_query_func.R R/calc_het.R R/zip_datafiles.R R/probs_to_grid.R R/compare_genoprob.R R/arg_util.R R/clean_scan1.R R/interp_map.R R/bayes_int.R R/cbind_expand.R R/reduce_to_index_snps.R R/calc_kinship.R R/cbind_viterbi.R R/covariates.R R/fit1_pg.R R/drop_markers.R R/cbind_calc_genoprob.R R/calc_genoprob.R R/chr_lengths.R R/rbind_calc_genoprob.R R/find_peaks.R R/find_markerpos.R R/decomp_kinship.R R/fit1.R R/predict_snpgeno.R R/find_peaks_and_lodint.R R/batch_vec.R R/insert_pseudomarkers.R R/viterbi.R R/plot_snpasso.R R/clean.R R/map_to_grid.R R/plot_genoprobcomp.R R/est_map.R R/genoprob_to_alleleprob.R R/find_map_gaps.R R/scan1coef_pg.R R/rbind_sim_geno.R R/sim_geno.R R/calc_sdp.R R/recode_snps.R R/scan1_binary.R R/scan1blup_pg.R R/subset_chr.R R/reduce_markers.R R/est_herit.R R/replace_ids.R R/smooth_gmap.R R/calc_errorlod.R R/summary_cross2.R R/pull_genoprobint.R R/max_scan1.R R/qtl2version.R R/plot_snpasso_and_sdp.R R/guess_phase.R R/map_functions.R R/rbind_scan1.R R/plot_scan1.R R/CCcolors-data.R R/read_csv.R R/is_phase_known.R R/add_threshold.R R/is_same.R R/plot_lodpeaks.R R/scan1perm_pg.R R/convert2cross2.R R/xpos_scan1.R R/plot_genoprob.R R/assign_allele_codes.R R/reduce_map_gaps.R R/find_index_snp.R R/qtl2-package.R R/check_cross2.R R/plot_snpasso_sdp_and_genes.R R/index_snps.R R/subset_viterbi.R R/chisq_colpairs.R R/read_csv_numer.R R/batch_cols.R R/read_cross2.R R/cluster_util.R R/cbind_sim_geno.R R/scale_kinship.R R/scan1_pg.R R/snpprob_from_cross.R R/test_util.R R/mat2strata.R R/kinship_util.R R/plot_genes.R R/subset_sim_geno.R R/dim_calc_genoprob.R R/cbind_scan1.R R/myround.R R/scan1perm.R R/calc_raw_summaries.R R/plot_snpasso_and_genes.R R/locate_xo.R R/plot_coef.R R/find_ibd_segments.R R/scan1max.R R/subset_calc_genoprob.R R/maxmarg.R R/subset_scan1.R R/create_gene_query_func.R R/scan1.R R/plot_sdp.R R/hmm_util.R R/top_snps.R R/write_control_file.R R/compare_geno.R R/calc_genoprob2.R R/find_common_ids.R R/scan1snps.R R/subset_cross2.R R/plot_coef_and_lod.R R/align_scan1_map.R R/subset_ind.R R/weights_util.R R/qtl2-internal.R R/read_pheno.R R/genoprob_to_snpprob.R R/plot_onegeno.R R/get_common_ids.R

src/random.h

src/scan1coef_hk.h

src/compare_geno.h

src/binreg_eigen.cpp

src/matrix.h

src/cross_ailpk.h

src/cross_riself.h

src/cross_genril.h

src/cross_f2pk.h

src/scan1coef_pg.h

src/binreg.cpp

src/cross_do.cpp

src/hmm_forwback2.cpp

src/cross_risib8.cpp

src/hmm_viterbi2.cpp

src/cross_f2.h

src/binreg_weighted_eigen.cpp

src/lmm.h

src/cross_do_util.cpp

src/cross.h

src/cross_util.h

src/find_peaks.cpp

src/clean_genoprob.h

src/debug_util.cpp

src/genoprob_to_alleleprob.cpp

src/hmm_estmap2.h

src/RcppExports.cpp

src/scan1coef_binary.cpp

src/hmm_forwback.h

src/cross_hsf1.cpp

src/hmm_viterbi.cpp

src/hmm_simgeno.cpp

src/brent_fmin.h

src/cross_dof1.cpp

src/reduce_markers.cpp

src/hmm_calcgenoprob.cpp

src/find_peaks.h

src/scan1coef_hk.cpp

src/hmm_forwback.cpp

src/scan1_hk.h

src/cross_riself4.h

src/cross_riself8.cpp

src/check_cross.cpp

src/hmm_calcgenoprob2.cpp

src/check_cross.h

src/predict_snpgeno.cpp

src/cross_magic19.cpp

src/binreg_eigen.h

src/debug_util.h

src/fit1_hk.h

src/hmm_util.cpp

src/cross_risib4.cpp

src/locate_xo.h

src/guess_phase.cpp

src/scan1_binary.h

src/interp_genoprob.cpp

src/cross_risib8.h

src/cross_util.cpp

src/count_xo.h

src/cross_ail.h

src/cross_riself4.cpp

src/linreg.cpp

src/cross_risib4.h

src/maxmarg.h

src/interpolate_maps.h

src/cross_do.h

src/scan1_pg.cpp

src/cross_hsf1.h

src/interp_genoprob.h

src/fit1_pg.h

src/cross_haploid.cpp

src/cross_bc.h

src/cross_hs.h

src/geno_names.h

src/hmm_forwback2.h

src/linreg.h

src/cross_dopk.h

src/binreg_weighted.h

src/hmm_simgeno2.h

src/hmm_estmap.h

src/binreg.h

src/chisq_colpairs.h

src/hmm_calcgenoprob2.h

src/hmm_viterbi.h

src/random.cpp

src/hmm_viterbi2.h

src/scan1_binary.cpp

src/bayes_int.cpp

src/hmm_estmap.cpp

src/r_message.h

src/compare_geno.cpp

src/scan1blup.h

src/scan1_pg.h

src/cross_dof1.h

src/snpprobs.h

src/get_x_covar.cpp

src/geno_names.cpp

src/linreg_eigen.cpp

src/cross_ail3pk.cpp

src/find_ibd_segments.h

src/lod_int.cpp

src/cross_riself8.h

src/test_hmm.cpp

src/cross_riself.cpp

src/bayes_int.h

src/count_xo.cpp

src/cross_riself16.cpp

src/cross_dh6.cpp

src/matrix.cpp

src/arrange_genes.h

src/cross_haploid.h

src/interpolate_maps.cpp

src/predict_snpgeno.h

src/cross_risib.h

src/scan1coef_binary.h

src/cross_hspk.cpp

src/hmm_estmap2.cpp

src/test_hmm.h

src/hmm_util.h

src/cross_f2.cpp

src/scan1blup.cpp

src/cross_genail.cpp

src/cross_genail.h

src/find_ibd_segments.cpp

src/cross_ailpk.cpp

src/cross_f2pk.cpp

src/cross_hs.cpp

src/arrange_genes.cpp

src/hmm_calcgenoprob.h

src/scan1_hk.cpp

src/cross_dh6.h

src/lod_int.h

src/fit1_binary.cpp

src/linreg_eigen.h

src/clean_genoprob.cpp

src/cross_bc.cpp

src/cross_ail3.h

src/scan1coef_pg.cpp

src/hmm_simgeno2.cpp

src/fit1_binary.h

src/brent_fmin.cpp

src/cross_genril.cpp

src/fit1_hk.cpp

src/cross_ail3.cpp

src/binreg_weighted.cpp

src/get_x_covar.h

src/r_message.cpp

src/fit1_pg.cpp

src/binreg_weighted_eigen.h

src/cross_riself16.h

src/cross_risib.cpp

src/cross.cpp

src/guess_phase.h

src/locate_xo.cpp

src/snpprobs.cpp

src/cross_ail.cpp

src/genoprob_to_alleleprob.h

src/lmm.cpp

src/cross_dh.h

src/hmm_calcerrorlod.h

src/cross_ail3pk.h

src/cross_magic19.h

src/cross_hspk.h

src/calc_kinship.h

src/hmm_calcerrorlod.cpp

src/hmm_simgeno.h

src/cross_do_util.h

src/maxmarg.cpp

src/chisq_colpairs.cpp

src/cross_dopk.cpp

src/reduce_markers.h

src/calc_kinship.cpp

inst/CITATION

inst/extdata/cc_variants_small.sqlite

inst/extdata/grav2.zip

inst/extdata/iron.zip

inst/extdata/ReadMe.md

inst/extdata/mouse_genes_small.sqlite

inst/scripts/create_mousegenes_small.R inst/scripts/create_mousegenes_mgi.R inst/scripts/create_mousegenes.R inst/scripts/create_ccvariants.R inst/scripts/create_ccvariants_small.R inst/scripts/ReadMe.md

build/partial.rdb

tests/testthat.R tests/testthat/test-drop_markers.R tests/testthat/test-hmmbasic-risib.R tests/testthat/test-calcgenoprob.R tests/testthat/test-mat2strata.R tests/testthat/test-xpos_scan1.R tests/testthat/test-scan1blup.R tests/testthat/test-scan1coef.R tests/testthat/test-hmmbasic-dh6.R tests/testthat/test-scan1perm.R tests/testthat/test-rcbind_simgeno.R tests/testthat/test-smooth_gmap.R tests/testthat/helper-utils.R tests/testthat/test-find_index_snp.R tests/testthat/test-est_herit.R tests/testthat/test-scanhk.R tests/testthat/test-linreg.R tests/testthat/test-basic_summaries.R tests/testthat/test-plot_genes.R tests/testthat/test-reduced_rank_covar_scan.R tests/testthat/test-hmmbasic-dh.R tests/testthat/test-create_marker_index.R tests/testthat/test-hmmbasic-dof1.R tests/testthat/test-plot_genoprob.R tests/testthat/test-expand_snp_results.R tests/testthat/test-reduce_map_gaps.R tests/testthat/test-scan1coef_pg.R tests/testthat/test-fit1.R tests/testthat/test-compare_geno.R tests/testthat/test-compare_maps.R tests/testthat/test-probs_to_grid.R tests/testthat/test-calc_entropy.R tests/testthat/test-mapfunc.R tests/testthat/test-hmmbasic-ail3pk.R tests/testthat/test-calcerrorlod.R tests/testthat/test-reduce_to_indexed_snps.R tests/testthat/test-hmmbasic-hs.R tests/testthat/test-create_variant_query_func.R tests/testthat/test-cross_util.R tests/testthat/test-hmmbasic-hsf1.R tests/testthat/test-guess_phase.R tests/testthat/test-assign_allele_codes.R tests/testthat/test-addlog.R tests/testthat/test-calc_grid.R tests/testthat/test-scan1_pg.R tests/testthat/test-pseudomarkermap.R tests/testthat/test-calc_geno_freq.R tests/testthat/test-reduce_markers.R tests/testthat/test-get_common_ids.R tests/testthat/test-read_issues.R tests/testthat/test-simgeno.R tests/testthat/test-subset_scan1.R tests/testthat/test-get_x_covar.R tests/testthat/test-hmmbasic-ail.R tests/testthat/test-binreg.R tests/testthat/test-chisq_colpairs.R tests/testthat/test-batch_cols.R tests/testthat/test-matrix.R tests/testthat/test-interpmap.R tests/testthat/test-pull_genoprobpos.R tests/testthat/test-genoprob_to_alleleprob.R tests/testthat/test-calc_sdp.R tests/testthat/test-drop_depcols.R tests/testthat/test-crossinfo_sex.R tests/testthat/test-is_phase_known.R tests/testthat/test-lmm.R tests/testthat/test-pull_genoprobint.R tests/testthat/test-create_snpinfo.R tests/testthat/test-hmmbasic-riself4-8-16.R tests/testthat/test-viterbi.R tests/testthat/test-arrange_genes.R tests/testthat/test-summary_scan1perm.R tests/testthat/test-hmmbasic-bc.R tests/testthat/test-hmmbasic-haploid.R tests/testthat/test-plot_pxg.R tests/testthat/test-subset.R tests/testthat/test-kinship_util.R tests/testthat/test-maxmarg.R tests/testthat/test-hmmbasic-magic19.R tests/testthat/test-scan1perm_binary.R tests/testthat/test-plot_peaks.R tests/testthat/test-count_xo.R tests/testthat/test-hmmbasic-riself.R tests/testthat/test-scan1snps.R tests/testthat/test-plot_coef.R tests/testthat/test-io.R tests/testthat/test-hmmbasic-do.R tests/testthat/test-hmmbasic-f2.R tests/testthat/test-hmmbasic-f2pk.R tests/testthat/test-predict_snpgeno.R tests/testthat/test-find_peaks.R tests/testthat/test-hmmbasic-dopk.R tests/testthat/test-check_cross.R tests/testthat/test-plot_scan1.R tests/testthat/test-find_ibd_segments.R tests/testthat/test-find_common_ids.R tests/testthat/test-estmap.R tests/testthat/test-plot_sdp.R tests/testthat/test-n_missing.R tests/testthat/test-find_marker.R tests/testthat/test-recode_snps.R tests/testthat/test-hmmbasic-genail.R tests/testthat/test-replace_ids.R tests/testthat/test-clean_scan1.R tests/testthat/test-top_snps.R tests/testthat/test-rcbind_scan1perm.R tests/testthat/test-force_intcovar.R tests/testthat/test-cbind_expand.R tests/testthat/test-rcbind_viterbi.R tests/testthat/test-align_scan1_map.R tests/testthat/test-hmmbasic-genril.R tests/testthat/test-decomp_kinship.R tests/testthat/test-genoprobs_col2drop.R tests/testthat/test-calc_kinship.R tests/testthat/test-scale_kinship.R tests/testthat/test-subset_kinship.R tests/testthat/test-zip_datafiles.R tests/testthat/test-hmmbasic-ailpk.R tests/testthat/test-chr_lengths.R tests/testthat/test-rcbind_calcgenoprob.R tests/testthat/test-hmmbasic-risib4-8.R tests/testthat/test-scan1max.R tests/testthat/test-max_scan1.R tests/testthat/test-calc_het.R tests/testthat/test-convert2cross2.R tests/testthat/test-map_to_pos.R tests/testthat/test-snpprobs.R tests/testthat/test-calc_raw_summaries.R tests/testthat/test-map_to_grid.R tests/testthat/test-hmmbasic-hspk.R tests/testthat/test-find_map_gaps.R tests/testthat/test-interp_genoprob.R tests/testthat/test-estmap2.R tests/testthat/test-create_gene_query_func.R tests/testthat/test-scan1_binary.R tests/testthat/test-index_snps.R tests/testthat/test-hmmbasic-ail3.R tests/testthat/test-rcbind_scan1.R tests/testthat/test-calcgenoprob2.R tests/testthat/test-clean_genoprob.R tests/testthat/test-fit1_binary.R tests/testthat/test-scan1.R tests/testthat/test-control_files.R tests/testthat/test-scan1coef_binary.R tests/testthat/test-is_same.R

tests/testthat/_snaps/plot_scan1/plot-scan1-onechr.svg

tests/testthat/_snaps/plot_scan1/plot-scan1.svg

tests/testthat/_snaps/plot_genoprob/plot-genoprob.svg

tests/testthat/_snaps/plot_pxg/plot-pxg-se.svg

tests/testthat/_snaps/plot_pxg/plot-pxg.svg

tests/testthat/_snaps/plot_genes/plot-genes.svg

tests/testthat/_snaps/plot_coef/plot-coef.svg

tests/testthat/_snaps/plot_sdp/plot-sdp.svg

tests/testthat/_snaps/plot_peaks/plot-peaks.svg

tests/testthat/_snaps/plot_peaks/plot-peaks-noci.svg

data/CCcolors.RData

data/CCorigcolors.RData

data/CCaltcolors.RData

man/batch_cols.Rd man/convert2cross2.Rd man/viterbi.Rd man/find_map_gaps.Rd man/interp_map.Rd man/scan1coef.Rd man/clean_scan1.Rd man/subset.sim_geno.Rd man/add_threshold.Rd man/cbind.viterbi.Rd man/find_index_snp.Rd man/read_cross2.Rd man/calc_errorlod.Rd man/maxlod.Rd man/n_missing.Rd man/cbind.scan1perm.Rd man/genoprob_to_snpprob.Rd man/scan1blup.Rd man/reduce_markers.Rd man/pull_markers.Rd man/subset.viterbi.Rd man/plot_sdp.Rd man/batch_vec.Rd man/subset.calc_genoprob.Rd man/rbind.sim_geno.Rd man/guess_phase.Rd man/plot_compare_geno.Rd man/fit1.Rd man/create_snpinfo.Rd man/plot_genes.Rd man/est_herit.Rd man/basic_summaries.Rd man/maxmarg.Rd man/compare_maps.Rd man/create_gene_query_func.Rd man/compare_geno.Rd man/lod_int.Rd man/calc_entropy.Rd man/check_cross2.Rd man/plot_pxg.Rd man/read_csv.Rd man/chr_lengths.Rd man/map_to_grid.Rd man/scale_kinship.Rd man/scan1perm.Rd man/drop_markers.Rd man/calc_genoprob.Rd man/pull_genoprobint.Rd man/replace_ids.Rd man/sim_geno.Rd man/calc_het.Rd man/compare_genoprob.Rd man/predict_snpgeno.Rd man/cbind.scan1.Rd man/qtl2-package.Rd man/scan1max.Rd man/summary.cross2.Rd man/plot_peaks.Rd man/pull_genoprobpos.Rd man/est_map.Rd man/print.summary.scan1perm.Rd man/top_snps.Rd man/max_compare_geno.Rd man/plot_lodpeaks.Rd man/calc_raw_het.Rd man/probs_to_grid.Rd man/zip_datafiles.Rd man/find_ibd_segments.Rd man/plot_onegeno.Rd man/invert_sdp.Rd man/bayes_int.Rd man/read_pheno.Rd man/scan1.Rd man/clean_genoprob.Rd man/clean.Rd man/genoprob_to_alleleprob.Rd man/recode_snps.Rd man/calc_kinship.Rd man/create_variant_query_func.Rd man/summary_scan1perm.Rd man/interp_genoprob.Rd man/reduce_map_gaps.Rd man/chisq_colpairs.Rd man/print.cross2.Rd man/calc_raw_maf.Rd man/cbind.calc_genoprob.Rd man/calc_raw_geno_freq.Rd man/summary_compare_geno.Rd man/plot_snpasso.Rd man/find_peaks.Rd man/insert_pseudomarkers.Rd man/decomp_kinship.Rd man/max_scan1.Rd man/cbind.sim_geno.Rd man/calc_grid.Rd man/smooth_gmap.Rd man/write_control_file.Rd man/plot_genoprobcomp.Rd man/scan1snps.Rd man/unsmooth_gmap.Rd man/qtl2version.Rd man/plot_genoprob.Rd man/calc_sdp.Rd man/mat2strata.Rd man/xpos_scan1.Rd man/get_x_covar.Rd man/rbind.calc_genoprob.Rd man/drop_nullmarkers.Rd man/get_common_ids.Rd man/cbind_expand.Rd man/calc_geno_freq.Rd man/plot_scan1.Rd man/sdp2char.Rd man/read_csv_numer.Rd man/plot_coef.Rd man/calc_raw_founder_maf.Rd man/index_snps.Rd man/find_markerpos.Rd man/rbind.scan1.Rd man/rbind.viterbi.Rd man/CCcolors.Rd man/count_xo.Rd man/locate_xo.Rd man/subset_scan1.Rd man/qtl2-internal.Rd man/rbind.scan1perm.Rd man/subset.cross2.Rd man/find_marker.Rd

qtl2 documentation built on April 22, 2023, 1:10 a.m.