add_dup_markers	add_dup_markers
ALL_dosages	ALL_dosages
all_linkages_list_P1	all_linkages_list_P1
all_linkages_list_P1_split	all_linkages_list_P1
all_linkages_list_P1_subset	all_linkages_list_P1
assembleDuplexLinks	bridgeHomologues
assign_linkage_group	assign_linkage_group
assign_SN_SN	assign_SN_SN
bridgeHomologues	bridgeHomologues
calcSegtypeInfo	calcSegtypeInfo
checkF1	checkF1
check_map	check_map
check_marker_assignment	check_marker_assignment
check_maxP	check_maxP
chk1	chk1
cluster_per_LG	cluster_per_LG
cluster_SN_markers	cluster_SN_markers
compare_maps	compare_maps
consensus_LG_assignment	consensus_LG_assignment
consensus_LG_names	consensus_LG_names
convert_marker_dosages	convert_marker_dosages
convert_polyRAD	convert_polyRAD
convert_updog	convert_updog
correctDosages	correctDosages
createTetraOriginInput	createTetraOriginInput
create_phased_maplist	create_phased_maplist
define_LG_structure	define_LG_structure
exampleRAD_mapping	exampleRAD_mapping
finish_linkage_analysis	finish_linkage_analysis
get_markertype_combinations	get_markertype_combinations
gp_df	gp_df
gp_overview	gp_overview
homologue_lg_assignment	homologue_lg_assignment
integrated.maplist	integrated.maplist
LGHomDf_P1_1	LGHomDf_P1_1
LGHomDf_P2_1	LGHomDf_P1_1
LGHomDf_P2_2	LGHomDf_P1_1
linkage	linkage
linkage.gp	linkage.gp
map1	map1
map2	map2
map3	map3
maplist_P1	maplist_P1
maplist_P1_subset	maplist_P1
maplist_P2_subset	maplist_P1
marker_assignments_P1	P1_SxS_Assigned
marker_assignments_P2	P1_SxS_Assigned
marker_binning	marker_binning
marker_data_summary	marker_data_summary
MDSMap_from_list	MDSMap_from_list
merge_homologues	merge_homologues
merge_marker_assignments	merge_marker_assignments
mout	mout
overviewSNlinks	overviewSNlinks
P1_DxN_Assigned	P1_SxS_Assigned
P1_homologues	P1_homologues
P1_SxS_Assigned	P1_SxS_Assigned
P2_DxN_Assigned	P1_SxS_Assigned
P2_homologues	P1_homologues
P2_homologues_triploid	P1_homologues
P2_SxS_Assigned	P1_SxS_Assigned
P2_SxS_Assigned_2	P1_SxS_Assigned
p4_functions	p4_functions
parental_quantities	parental_quantities
PCA_progeny	PCA_progeny
phased.maplist	phased.maplist
phase_SN_diploid	phase_SN_diploid
plot_hom_vs_LG	plot_hom_vs_LG
plot_linkage_df	plot_linkage_df
plot_map	plot_map
plot_phased_maplist	plot_phased_maplist
polymapR	polymapR
r2_1.0_1.0	r2_functions
r2_1.0_1.1	r2_functions
r2_1.1_1.1	r2_functions
r2_functions	r2_functions
r3_0.1_0.1	r3_functions
r3_0.1_1.1	r3_functions
r3_0.1_2.1	r3_functions
r3_2.1_2.1	r3_functions
r3_functions	r3_functions
r4_functions	r4_functions
r6_functions	r6_functions
r_LOD_plot	r_LOD_plot
screened_data	ALL_dosages
screened_data2	ALL_dosages
screened_data3	ALL_dosages
screen_for_duplicate_individuals	screen_for_duplicate_individuals
screen_for_duplicate_individuals.gp	screen_for_duplicate_individuals.gp
screen_for_duplicate_markers	screen_for_duplicate_markers
screen_for_NA_values	screen_for_NA_values
segregating_data	ALL_dosages
SNSN_LOD_deviations	SNSN_LOD_deviations
SN_DN_P1	SN_SN_P1
SN_DN_P2	SN_SN_P1
SN_SN_P1	SN_SN_P1
SN_SN_P2	SN_SN_P1
SN_SN_P2_triploid	SN_SN_P1
SN_SS_P1	SN_SN_P1
SN_SS_P2	SN_SN_P1
test_prefpairing	test_prefpairing
TRI_dosages	ALL_dosages
write.mct	write.mct
write.pwd	write.pwd
write.TSNPM	write.TSNPM
write_nested_list	write_nested_list
write_pwd_list	write_pwd_list
