Files in rqtl/qtl2geno

Treatment of Marker Genotypes for QTL Experiments

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

License.md

Makefile

NAMESPACE

NEWS.md R/RcppExports.R R/assign_allele_codes.R R/calc_entropy.R R/calc_errorlod.R R/calc_geno_freq.R R/calc_genoprob.R R/calc_genoprob2.R R/calc_grid.R R/calc_kinship.R R/cbind_calc_genoprob.R R/cbind_expand.R R/cbind_sim_geno.R R/cbind_viterbi.R R/check_cross2.R R/chisq_colpairs.R R/cluster_util.R R/compare_geno.R R/compare_genoprob.R R/convert2cross2.R R/count_xo.R R/create_marker_index.R R/dim_calc_genoprob.R R/drop_markers.R R/est_map.R R/find_common_ids.R R/find_ibd_segments.R R/find_map_gaps.R R/find_marker.R R/find_markerpos.R R/genoprob_to_alleleprob.R R/get_x_covar.R R/guess_phase.R R/hmm_util.R R/insert_pseudomarkers.R R/interp_genoprob.R R/is_phase_known.R R/is_same.R R/locate_xo.R R/map_functions.R R/map_to_grid.R R/maxmarg.R R/n_missing.R R/probs_to_grid.R R/qtl2geno-package.R R/rbind_calc_genoprob.R R/rbind_sim_geno.R R/rbind_viterbi.R R/read_cross2.R R/read_csv.R R/read_csv_numer.R R/read_pheno.R R/reduce_map_gaps.R R/reduce_markers.R R/scale_kinship.R R/sim_geno.R R/sim_geno2.R R/subset_calc_genoprob.R R/subset_chr.R R/subset_cross2.R R/subset_ind.R R/subset_sim_geno.R R/subset_viterbi.R R/summary_cross2.R R/test_util.R R/viterbi.R R/viterbi2.R R/write_control_file.R R/zip_datafiles.R ReadMe.md inst/License.md inst/ReadMe.md inst/extdata/ReadMe.md

inst/extdata/grav2.zip

inst/extdata/iron.zip

man/basic_summaries.Rd man/calc_entropy.Rd man/calc_errorlod.Rd man/calc_geno_freq.Rd man/calc_genoprob.Rd man/calc_grid.Rd man/calc_kinship.Rd man/cbind.calc_genoprob.Rd man/cbind.sim_geno.Rd man/cbind.viterbi.Rd man/check_cross2.Rd man/chisq_colpairs.Rd man/compare_geno.Rd man/compare_genoprob.Rd man/convert2cross2.Rd man/count_xo.Rd man/drop_markers.Rd man/drop_nullmarkers.Rd man/est_map.Rd man/find_ibd_segments.Rd man/find_map_gaps.Rd man/find_marker.Rd man/find_markerpos.Rd man/genoprob_to_alleleprob.Rd man/get_x_covar.Rd man/guess_phase.Rd man/insert_pseudomarkers.Rd man/interp_genoprob.Rd man/locate_xo.Rd man/map_to_grid.Rd man/max_compare_geno.Rd man/maxmarg.Rd man/n_missing.Rd man/print.cross2.Rd man/probs_to_grid.Rd man/pull_markers.Rd man/qtl2geno-package.Rd man/rbind.calc_genoprob.Rd man/rbind.sim_geno.Rd man/rbind.viterbi.Rd man/read_cross2.Rd man/read_csv.Rd man/read_csv_numer.Rd man/read_pheno.Rd man/reduce_map_gaps.Rd man/reduce_markers.Rd man/scale_kinship.Rd man/sim_geno.Rd man/subset.calc_genoprob.Rd man/subset.cross2.Rd man/subset.sim_geno.Rd man/subset.viterbi.Rd man/summary.cross2.Rd man/summary_compare_geno.Rd man/viterbi.Rd man/write_control_file.Rd man/zip_datafiles.Rd

src/RcppExports.cpp

src/calc_kinship.cpp

src/calc_kinship.h

src/check_cross.cpp

src/check_cross.h

src/chisq_colpairs.cpp

src/chisq_colpairs.h

src/compare_geno.cpp

src/compare_geno.h

src/count_xo.cpp

src/count_xo.h

src/cross.cpp

src/cross.h

src/cross_ail.cpp

src/cross_ail.h

src/cross_ail3.cpp

src/cross_ail3.h

src/cross_ail3pk.cpp

src/cross_ail3pk.h

src/cross_ailpk.cpp

src/cross_ailpk.h

src/cross_bc.cpp

src/cross_bc.h

src/cross_dh.h

src/cross_dh6.cpp

src/cross_dh6.h

src/cross_do.cpp

src/cross_do.h

src/cross_do_util.cpp

src/cross_do_util.h

src/cross_dof1.cpp

src/cross_dof1.h

src/cross_dopk.cpp

src/cross_dopk.h

src/cross_f2.cpp

src/cross_f2.h

src/cross_f2pk.cpp

src/cross_f2pk.h

src/cross_haploid.cpp

src/cross_haploid.h

src/cross_hs.cpp

src/cross_hs.h

src/cross_hspk.cpp

src/cross_hspk.h

src/cross_magic19.cpp

src/cross_magic19.h

src/cross_riself.cpp

src/cross_riself.h

src/cross_riself16.cpp

src/cross_riself16.h

src/cross_riself4.cpp

src/cross_riself4.h

src/cross_riself8.cpp

src/cross_riself8.h

src/cross_risib.cpp

src/cross_risib.h

src/cross_risib4.cpp

src/cross_risib4.h

src/cross_risib8.cpp

src/cross_risib8.h

src/cross_util.cpp

src/cross_util.h

src/find_ibd_segments.cpp

src/find_ibd_segments.h

src/geno_names.cpp

src/geno_names.h

src/genoprob_to_alleleprob.cpp

src/genoprob_to_alleleprob.h

src/get_x_covar.cpp

src/get_x_covar.h

src/guess_phase.cpp

src/guess_phase.h

src/hmm_calcerrorlod.cpp

src/hmm_calcerrorlod.h

src/hmm_calcgenoprob.cpp

src/hmm_calcgenoprob.h

src/hmm_calcgenoprob2.cpp

src/hmm_calcgenoprob2.h

src/hmm_estmap.cpp

src/hmm_estmap.h

src/hmm_estmap2.cpp

src/hmm_estmap2.h

src/hmm_forwback.cpp

src/hmm_forwback.h

src/hmm_forwback2.cpp

src/hmm_forwback2.h

src/hmm_simgeno.cpp

src/hmm_simgeno.h

src/hmm_simgeno2.cpp

src/hmm_simgeno2.h

src/hmm_util.cpp

src/hmm_util.h

src/hmm_viterbi.cpp

src/hmm_viterbi.h

src/hmm_viterbi2.cpp

src/hmm_viterbi2.h

src/interp_genoprob.cpp

src/interp_genoprob.h

src/locate_xo.cpp

src/locate_xo.h

src/maxmarg.cpp

src/maxmarg.h

src/r_message.cpp

src/r_message.h

src/random.cpp

src/random.h

src/reduce_markers.cpp

src/reduce_markers.h

src/test_hmm.cpp

src/test_hmm.h

tests/testthat.R tests/testthat/test-addlog.R tests/testthat/test-assign_allele_codes.R tests/testthat/test-basic_summaries.R tests/testthat/test-calc_entropy.R tests/testthat/test-calc_geno_freq.R tests/testthat/test-calc_grid.R tests/testthat/test-calc_kinship.R tests/testthat/test-calcerrorlod.R tests/testthat/test-calcgenoprob.R tests/testthat/test-calcgenoprob2.R tests/testthat/test-cbind_expand.R tests/testthat/test-check_cross.R tests/testthat/test-chisq_colpairs.R tests/testthat/test-compare_geno.R tests/testthat/test-control_files.R tests/testthat/test-convert2cross2.R tests/testthat/test-convert_sexcodes.R tests/testthat/test-count_xo.R tests/testthat/test-create_marker_index.R tests/testthat/test-cross_util.R tests/testthat/test-crossinfo_sex.R tests/testthat/test-drop_markers.R tests/testthat/test-estmap.R tests/testthat/test-estmap2.R tests/testthat/test-find_common_ids.R tests/testthat/test-find_ibd_segments.R tests/testthat/test-find_map_gaps.R tests/testthat/test-find_marker.R tests/testthat/test-genoprob_to_alleleprob.R tests/testthat/test-get_x_covar.R tests/testthat/test-guess_phase.R tests/testthat/test-hmmbasic-ail.R tests/testthat/test-hmmbasic-ail3.R tests/testthat/test-hmmbasic-ail3pk.R tests/testthat/test-hmmbasic-ailpk.R tests/testthat/test-hmmbasic-bc.R tests/testthat/test-hmmbasic-dh.R tests/testthat/test-hmmbasic-dh6.R tests/testthat/test-hmmbasic-do.R tests/testthat/test-hmmbasic-dof1.R tests/testthat/test-hmmbasic-dopk.R tests/testthat/test-hmmbasic-f2.R tests/testthat/test-hmmbasic-f2pk.R tests/testthat/test-hmmbasic-haploid.R tests/testthat/test-hmmbasic-hs.R tests/testthat/test-hmmbasic-hspk.R tests/testthat/test-hmmbasic-magic19.R tests/testthat/test-hmmbasic-riself.R tests/testthat/test-hmmbasic-riself4-8-16.R tests/testthat/test-hmmbasic-risib.R tests/testthat/test-hmmbasic-risib4-8.R tests/testthat/test-interp_genoprob.R tests/testthat/test-io.R tests/testthat/test-is_phase_known.R tests/testthat/test-is_same.R tests/testthat/test-map_to_grid.R tests/testthat/test-mapfunc.R tests/testthat/test-maxmarg.R tests/testthat/test-n_missing.R tests/testthat/test-probs_to_grid.R tests/testthat/test-pseudomarkermap.R tests/testthat/test-rcbind_calcgenoprob.R tests/testthat/test-rcbind_simgeno.R tests/testthat/test-rcbind_viterbi.R tests/testthat/test-read_issues.R tests/testthat/test-reduce_map_gaps.R tests/testthat/test-reduce_markers.R tests/testthat/test-scale_kinship.R tests/testthat/test-simgeno.R tests/testthat/test-subset.R tests/testthat/test-viterbi.R

rqtl/qtl2geno documentation built on May 28, 2019, 2:36 a.m.