Files in onemap
Construction of Genetic Maps in Experimental Crosses
MD5
NAMESPACE
DESCRIPTION
R/plot_raw_data.R
R/avoid_reverse.R
R/draw_map.R
R/write_map.R
R/draw_map2.R
R/permutations.R
R/marker_type.R
R/rf_2pts.R
R/ripple_seq.R
R/adjust_rils.R
R/group.R
R/filters.R
R/extract_depth.R
R/test_segregation.R
R/create_dataset_bins.R
R/create_probs.R
R/drop_marker.R
R/map.R
R/read_onemap.R
R/group_upgma.R
R/combine_onemap.R
R/get_info_2pt.R
R/write_haplotypes.R
R/record.R
R/ug.R
R/create_depths_profile.R
R/return_geno.R
R/try_seq.R
R/map_func.R
R/group_seq.R
R/read_mapmaker.R
R/overlapping_batches.R
R/onemap_read_vcfR.R
R/comb_ger.R
R/mds_onemap.R
R/make_seq.R
R/order_seq.R
R/find_bins.R
R/zzz.R
R/cpp_utils.R
R/vcf2raw.R
R/rf_graph_table.R
R/rcd.R
R/codif_data.R
R/phases.R
R/compare.R
R/utils.R
R/seriation.R
R/suggest_lod.R
R/seeded_map.R
src/Makevars.win
src/hmm_bc.cpp
src/twopts_out.h
src/twopts_bc.cpp
src/twopts_bc.h
src/onemap_init.c
src/twopts_out.cpp
src/hmm_bc.h
src/hmm_out.h
src/utils.cpp
src/hmm_f2.h
src/find_bins.cpp
src/utils.h
src/hmm_f2.cpp
src/out_est.cpp
src/hmm_out.cpp
src/out_est.h
src/find_bins.h
inst/CITATION
inst/doc/Outcrossing_Populations.html
inst/doc/Outcrossing_Populations.R
inst/doc/Introduction_R.Rmd
inst/doc/Outcrossing_Populations.Rmd
inst/doc/Overview.R
inst/doc/Introduction_R.html
inst/doc/Overview.html
inst/doc/Introduction_R.R
inst/doc/Overview.Rmd
inst/doc/Inbred_Based_Populations.html
inst/doc/Inbred_Based_Populations.Rmd
inst/doc/Inbred_Based_Populations.R
inst/extdata/mapmaker_example_bc.raw
inst/extdata/vcf_example_out.raw
inst/extdata/vcf_example_f2.raw
inst/extdata/vcf_example_f2.vcf.gz.tbi
inst/extdata/onemap_example_riself.raw
inst/extdata/onemap_example_out.raw
inst/extdata/vcf_example_f2.vcf.gz
inst/extdata/onemap_example_f2.raw
inst/extdata/mapmaker_example_f2.raw
inst/extdata/onemap_example_bc.raw
inst/extdata/vcf_example_out.vcf.gz
inst/extdata/vcf_example_out.vcf.gz.tbi
build/vignette.rds
build/partial.rdb
vignettes/Introduction_R.Rmd
vignettes/Outcrossing_Populations.Rmd
vignettes/Overview.Rmd
vignettes/Inbred_Based_Populations.Rmd
vignettes/f2_img/ug.jpg
vignettes/f2_img/record.jpg
vignettes/f2_img/map.jpg
vignettes/f2_img/rcd.jpg
vignettes/f2_img/mds.jpg
vignettes/out_img/plot.segre.jpg
vignettes/out_img/ug.jpg
vignettes/out_img/record.jpg
vignettes/out_img/map.jpg
vignettes/out_img/rcd.jpg
vignettes/out_img/plot.simParallel.jpg
vignettes/out_img/mds.jpg
data/mapmaker_example_f2.RData
data/vcf_example_out.RData
data/onemap_example_f2.RData
data/vcf_example_f2.RData
data/onemap_example_riself.RData
data/onemap_example_bc.RData
data/onemap_example_out.RData
data/vcf_example_riself.RData
data/vcf_example_bc.RData
man/vcf2raw.Rd
man/order_seq.Rd
man/print.onemap_bin.Rd
man/draw_map.Rd
man/kosambi.Rd
man/onemap_read_vcfR.Rd
man/compare.Rd
man/plot.onemap_progeny_haplotypes_counts.Rd
man/print.onemap_segreg_test.Rd
man/extract_depth.Rd
man/rm_dupli_mks.Rd
man/print.group.Rd
man/create_data_bins.Rd
man/plot.onemap_progeny_haplotypes.Rd
man/est_map_hmm_out.Rd
man/drop_marker.Rd
man/print.sequence.Rd
man/filter_missing.Rd
man/make_seq.Rd
man/progeny_haplotypes_counts.Rd
man/progeny_haplotypes.Rd
man/plot.onemap.Rd
man/set_map_fun.Rd
man/filter_2pts_gaps.Rd
man/map_avoid_unlinked.Rd
man/vcf_example_bc.Rd
man/find_bins.Rd
man/filter_prob.Rd
man/add_marker.Rd
man/create_depths_profile.Rd
man/split_onemap.Rd
man/Bonferroni_alpha.Rd
man/onemap_example_f2.Rd
man/test_segregation_of_a_marker.Rd
man/check_data.Rd
man/vcf_example_riself.Rd
man/map.Rd
man/map_save_ram.Rd
man/print.group_seq.Rd
man/plot_by_segreg_type.Rd
man/plot.onemap_segreg_test.Rd
man/rf_2pts.Rd
man/record.Rd
man/draw_map2.Rd
man/print.try.Rd
man/pick_batch_sizes.Rd
man/write_onemap_raw.Rd
man/print.onemap.Rd
man/mds_onemap.Rd
man/remove_inds.Rd
man/write_map.Rd
man/keep_only_selected_mks.Rd
man/empty_onemap_obj.Rd
man/ripple_seq.Rd
man/check_twopts.Rd
man/print.order.Rd
man/onemap_example_riself.Rd
man/sort_by_pos.Rd
man/map_overlapping_batches.Rd
man/acum.Rd
man/ug.Rd
man/combine_onemap.Rd
man/split_2pts.Rd
man/plot.group.upgma.Rd
man/haldane.Rd
man/suggest_lod.Rd
man/read_onemap.Rd
man/select_segreg.Rd
man/add_redundants.Rd
man/print.rf_2pts.Rd
man/seq_by_type.Rd
man/mapmaker_example_f2.Rd
man/print.group.upgma.Rd
man/generate_overlapping_batches.Rd
man/try_seq_by_seq.Rd
man/create_dataframe_for_plot_outcross.Rd
man/create_probs.Rd
man/rf_snp_filter_onemap.Rd
man/rf_graph_table.Rd
man/marker_type.Rd
man/vcf_example_out.Rd
man/onemap_example_out.Rd
man/rcd.Rd
man/read_mapmaker.Rd
man/group.Rd
man/group_upgma.Rd
man/parents_haplotypes.Rd
man/test_segregation.Rd
man/print.compare.Rd
man/group_seq.Rd
man/onemap_example_bc.Rd
man/vcf_example_f2.Rd
man/try_seq.Rd
man/seriation.Rd
man/seeded_map.Rd
