add_marker	add_marker
add_mrk_at_tail_ph_list	add_mrk_at_tail_ph_list
aggregate_matrix	aggregate_matrix
cache_counts_twopt	cache_counts_twopt
calc_genoprob	calc_genoprob
calc_genoprob_dist	calc_genoprob_dist
calc_genoprob_error	calc_genoprob_error
calc_genoprob_haplo	calc_genoprob_haplo
calc_genoprob_one_parent	calc_genoprob_one_parent
calc_homologprob	calc_homologprob
calc_prefpair_profiles	calc_prefpair_profiles
cat_phase	cat_phase
check_data_dist_sanity	check_data_dist_sanity
check_data_dose_sanity	check_data_dose_sanity
check_data_sanity	check_data_sanity
check_if_rf_is_possible	check_if_rf_is_possible
check_ls_phase	check_ls_phase
check_pairwise	check_pairwise
compare_haplotypes	compare_haplotypes
compare_maps	compare_maps
concatenate_new_marker	concatenate_new_marker
concatenate_ph_list	concatenate_ph_list
create_map	create_map
dist_prob_to_class	dist_prob_to_class
draw_cross	draw_cross
draw_phases	draw_phases
drop_marker	drop_marker
elim_conf_using_two_pts	elim_conf_using_two_pts
elim_equiv	elim_equiv
elim_redundant	elim_redundant
est_full_hmm_with_global_error	est_full_hmm_with_global_error
est_full_hmm_with_prior_prob	est_full_hmm_with_prior_prob
est_haplo_hmm	est_haplo_hmm
est_map_haplo_given_genoprob	est_map_haplo_given_genoprob
est_pairwise_rf	est_pairwise_rf
est_pairwise_rf2	est_pairwise_rf2
est_rf_hmm	est_rf_hmm
est_rf_hmm_sequential	est_rf_hmm_sequential
est_rf_hmm_single	est_rf_hmm_single
est_rf_hmm_single_one_parent	est_rf_hmm_single_one_parent
export_data_to_polymapR	export_data_to_polymapR
export_map_list	export_map_list
export_qtlpoly	export_qtlpoly
extract_map	extract_map
filter_individuals	filter_individuals
filter_map_at_hmm_thres	filter_map_at_hmm_thres
filter_missing	filter_missing
filter_missing_ind	filter_missing_ind
filter_missing_mrk	filter_missing_mrk
filter_non_conforming_classes	filter_non_conforming_classes
filter_segregation	filter_segregation
format_rf	format_rf
generate_all_link_phases_elim_equivalent_haplo	generate_all_link_phases_elim_equivalent_haplo
generate_all_link_phase_elim_equivalent	generate_all_link_phase_elim_equivalent
genotyping_global_error	genotyping_global_error
get_cache_two_pts_from_web	get_cache_two_pts_from_web
get_counts	get_counts
get_counts_all_phases	get_counts_all_phases
get_counts_one_parent	get_counts_one_parent
get_counts_two_parents	get_counts_two_parents
get_dosage_type	get_dosage_type
get_full_info_tail	get_full_info_tail
get_genomic_order	get_genomic_order
get_ij	get_ij
get_indices_from_selected_phases	get_indices_from_selected_phases
get_LOD	get_LOD
get_ols_map	get_ols_map
get_ph_conf_ret_sh	get_ph_conf_ret_sh
get_ph_list_subset	get_ph_list_subset
get_rf_from_list	get_rf_from_list
get_rf_from_mat	get_rf_from_mat
get_states_and_emission_one_parent	get_states_and_emission_one_parent
get_submap	get_submap
get_tab_mrks	get_tab_mrks
get_w_m	get_w_m
gg_color_hue	gg_color_hue
group_mappoly	group_mappoly
hexafake	hexafake
hexafake.geno.dist	hexafake.geno.dist
imf_h	imf_h
imf_k	imf_k
imf_m	imf_m
import_data_from_polymapR	import_data_from_polymapR
import_from_updog	import_from_updog
import_phased_maplist_from_polymapR	import_phased_maplist_from_polymapR
is.prob.data	is.prob.data
loglike_hmm	loglike_hmm
ls_linkage_phases	ls_linkage_phases
make_mat_mappoly	make_mat_mappoly
make_pairs_mappoly	make_pairs_mappoly
make_seq_mappoly	make_seq_mappoly
maps.hexafake	maps.hexafake
mds_mappoly	mds_mappoly
merge_datasets	merge_datasets
merge_maps	merge_maps
mf_h	mf_h
mf_k	mf_k
mf_m	mf_m
mrk_chisq_test	mrk_chisq_test
msg	msg
paralell_pairwise_discrete	paralell_pairwise_discrete
paralell_pairwise_discrete_rcpp	paralell_pairwise_discrete_rcpp
paralell_pairwise_probability	paralell_pairwise_probability
perm_pars	perm_pars
perm_tot	perm_tot
ph_list_to_matrix	ph_list_to_matrix
ph_matrix_to_list	ph_matrix_to_list
plot.mappoly.data	read_geno
plot.mappoly.geno.ord	get_genomic_order
plot.mappoly.homoprob	plot.mappoly.homoprob
plot.mappoly.map	est_rf_hmm
plot.mappoly.prefpair.profiles	plot.mappoly.prefpair.profiles
plot.mappoly.rf.matrix	rf_list_to_matrix
plot.mappoly.sequence	make_seq_mappoly
plot.two.pts.linkage.phases	ls_linkage_phases
plot_compare_haplotypes	plot_compare_haplotypes
plot_genome_vs_map	plot_genome_vs_map
plot_GIC	plot_GIC
plot_map_list	plot_map_list
plot_mrk_info	plot_mrk_info
plot_one_map	plot_one_map
poly_cross_simulate	poly_cross_simulate
poly_hmm_est	poly_hmm_est
prepare_map	prepare_map
print.mappoly.data	read_geno
print.mappoly.geno.ord	get_genomic_order
print.mappoly.map	est_rf_hmm
print.mappoly.pcmap	mds_mappoly
print.mappoly.pcmap3d	mds_mappoly
print.mappoly.rf.matrix	rf_list_to_matrix
print.mappoly.sequence	make_seq_mappoly
print.two.pts.linkage.phases	ls_linkage_phases
print_mrk	print_mrk
print_ph	print_ph
read_fitpoly	read_fitpoly
read_geno	read_geno
read_geno_csv	read_geno_csv
read_geno_prob	read_geno_prob
read_vcf	read_vcf
reest_rf	reest_rf
rev_map	rev_map
rf_list_to_matrix	rf_list_to_matrix
rf_snp_filter	rf_snp_filter
sample_data	sample_data
segreg_poly	segreg_poly
select_rf	select_rf
sim_cross_one_informative_parent	sim_cross_one_informative_parent
sim_cross_two_informative_parents	sim_cross_two_informative_parents
sim_homologous	sim_homologous
solcap.dose.map	solcap.dose.map
solcap.err.map	solcap.err.map
solcap.mds.map	solcap.mds.map
solcap.prior.map	solcap.prior.map
split_and_rephase	split_and_rephase
summary_maps	summary_maps
table_to_mappoly	table_to_mappoly
tetra.solcap	tetra.solcap
tetra.solcap.geno.dist	tetra.solcap.geno.dist
update_map	update_map
update_missing	update_missing
update_ph_list_at_hmm_thres	update_ph_list_at_hmm_thres
v_2_m	v_2_m
