polymapR-package	polymapR
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
calcPotShifts	calcPotShifts
calcSegtypeInfo	calcSegtypeInfo
calc_binning_thresholds	calc_binning_thresholds
calc_q1	calc_q1
calc_q2	calc_q2
calc_q3	calc_q3
calc_qall	calc_qall
checkF1	checkF1
checkFilename	checkFilename
check_map	check_map
check_marker_assignment	check_marker_assignment
chk2integer	chk2integer
cluster_per_LG	cluster_per_LG
cluster_SN_markers	cluster_SN_markers
colour.bar	colour.bar
consensus_LG_assignment	consensus_LG_assignment
consensus_LG_names	consensus_LG_names
convert_marker_dosages	convert_marker_dosages
correctDosages	correctDosages
createChmHomList	createChmHomList
createMap	createMap
createTetraOriginInput	createTetraOriginInput
create_phased_maplist	create_phased_maplist
define_LG_structure	define_LG_structure
digamfrq	digamfrq
finish_linkage_analysis	finish_linkage_analysis
gcd	gcd
gcd_all	gcd_all
getConsensusGeno	getConsensusGeno
getMatchParents	getMatchParents
get_markertype_combinations	get_markertype_combinations
homologue_lg_assignment	homologue_lg_assignment
integrated.maplist	integrated.maplist
leftstr	leftstr
LGHomDf_P1_1	LGHomDf_P1_1
LGHomDf_P2_1	LGHomDf_P1_1
LGHomDf_P2_2	LGHomDf_P1_1
linkage	linkage
linterpol	linterpol
makeProgeny	makeProgeny
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_binning_list	marker_binning_list
marker_data_summary	marker_data_summary
MDSMap_from_list	MDSMap_from_list
merge_homologues	merge_homologues
merge_marker_assignments	merge_marker_assignments
Mode	Mode
orient_and_merge_maps	orient_and_merge_maps
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_1.0_1.0	p4_functions
p4_1.0_1.1	p4_functions
p4_1.0_1.2	p4_functions
p4_1.0_1.3	p4_functions
p4_1.0_2.0	p4_functions
p4_1.0_2.1	p4_functions
p4_1.0_2.2	p4_functions
p4_1.1_1.1	p4_functions
p4_1.1_1.2	p4_functions
p4_1.1_1.3	p4_functions
p4_1.1_2.2	p4_functions
p4_1.2_1.2	p4_functions
p4_1.2_2.1	p4_functions
p4_1.2_2.2	p4_functions
p4_1.3_1.2	p4_functions
p4_1.3_1.3	p4_functions
p4_1.3_2.1	p4_functions
p4_1.3_2.2	p4_functions
p4_2.0_1.1	p4_functions
p4_2.0_1.2	p4_functions
p4_2.0_1.3	p4_functions
p4_2.0_2.0	p4_functions
p4_2.0_2.1	p4_functions
p4_2.0_2.2	p4_functions
p4_2.1_2.2	p4_functions
p4_2.2_2.2	p4_functions
p4_functions	p4_functions
p6_1.0_1.0	r6_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
plot_SNlinks	plot_SNlinks
polygamfrq	polygamfrq
polymapR	polymapR
prepare_pwd	prepare_pwd
r3_0.1_0.1	r3_functions
r3_0.1_1.1	r3_functions
r3_0.1_2.1	r3_functions
r3_1.0_1.0	r3_functions
r3_1.0_1.1	r3_functions
r3_1.0_2.0	r3_functions
r3_1.0_2.1	r3_functions
r3_1.1_1.1	r3_functions
r3_1.1_2.1	r3_functions
r3_2.0_1.1	r3_functions
r3_2.0_2.0	r3_functions
r3_2.0_2.1	r3_functions
r3_2.1_2.1	r3_functions
r3_functions	r3_functions
r4_1.0_1.0	r4_functions
r4_1.0_1.1	r4_functions
r4_1.0_1.2	r4_functions
r4_1.0_1.3	r4_functions
r4_1.0_2.0	r4_functions
r4_1.0_2.1	r4_functions
r4_1.0_2.2	r4_functions
r4_1.1_1.1	r4_functions
r4_1.1_1.2	r4_functions
r4_1.1_1.3	r4_functions
r4_1.1_2.2	r4_functions
r4_1.2_1.2	r4_functions
r4_1.2_2.1	r4_functions
r4_1.2_2.2	r4_functions
r4_1.3_1.2	r4_functions
r4_1.3_1.3	r4_functions
r4_1.3_2.1	r4_functions
r4_1.3_2.2	r4_functions
r4_2.0_1.1	r4_functions
r4_2.0_1.2	r4_functions
r4_2.0_1.3	r4_functions
r4_2.0_2.0	r4_functions
r4_2.0_2.1	r4_functions
r4_2.1_2.1	r4_functions
r4_2.1_2.2	r4_functions
r4_2.2_2.2	r4_functions
r4_functions	r4_functions
r6_1.0_1.0	r6_functions
r6_1.0_1.1	r6_functions
r6_1.0_1.2	r6_functions
r6_1.0_1.3	r6_functions
r6_1.0_1.4	r6_functions
r6_1.0_1.5	r6_functions
r6_1.0_2.0	r6_functions
r6_1.0_2.1	r6_functions
r6_1.0_2.2	r6_functions
r6_1.0_2.3	r6_functions
r6_1.0_2.4	r6_functions
r6_1.0_3.0	r6_functions
r6_1.0_3.1	r6_functions
r6_1.0_3.2	r6_functions
r6_1.0_3.3	r6_functions
r6_1.0_4.1	r6_functions
r6_1.1_1.1	r6_functions
r6_1.1_1.2	r6_functions
r6_1.1_1.3	r6_functions
r6_1.1_1.4	r6_functions
r6_1.1_1.5	r6_functions
r6_1.1_2.0	r6_functions
r6_1.1_2.2	r6_functions
r6_1.1_2.3	r6_functions
r6_1.1_2.4	r6_functions
r6_1.1_3.0	r6_functions
r6_1.1_3.3	r6_functions
r6_1.2_1.2	r6_functions
r6_1.2_1.3	r6_functions
r6_1.2_1.4	r6_functions
r6_1.2_1.5	r6_functions
r6_1.2_2.1	r6_functions
r6_1.2_2.2	r6_functions
r6_1.2_2.3	r6_functions
r6_1.2_2.4	r6_functions
r6_1.2_3.0	r6_functions
r6_1.2_3.1	r6_functions
r6_1.2_3.2	r6_functions
r6_1.2_3.3	r6_functions
r6_1.2_4.1	r6_functions
r6_1.3_1.3	r6_functions
r6_1.3_1.4	r6_functions
r6_1.3_1.5	r6_functions
r6_1.3_2.2	r6_functions
r6_1.3_2.3	r6_functions
r6_1.3_2.4	r6_functions
r6_1.3_3.1	r6_functions
r6_1.3_3.2	r6_functions
r6_1.3_3.3	r6_functions
r6_1.3_4.1	r6_functions
r6_1.4_1.4	r6_functions
r6_1.4_1.5	r6_functions
r6_1.4_2.2	r6_functions
r6_1.4_2.3	r6_functions
r6_1.4_2.4	r6_functions
r6_1.4_3.2	r6_functions
r6_1.4_3.3	r6_functions
r6_1.4_4.1	r6_functions
r6_1.5_1.5	r6_functions
r6_1.5_2.2	r6_functions
r6_1.5_2.3	r6_functions
r6_1.5_2.4	r6_functions
r6_1.5_3.2	r6_functions
r6_1.5_3.3	r6_functions
r6_2.0_1.2	r6_functions
r6_2.0_1.3	r6_functions
r6_2.0_1.4	r6_functions
r6_2.0_1.5	r6_functions
r6_2.0_2.0	r6_functions
r6_2.0_2.1	r6_functions
r6_2.0_2.2	r6_functions
r6_2.0_2.3	r6_functions
r6_2.0_2.4	r6_functions
r6_2.0_3.0	r6_functions
r6_2.0_3.1	r6_functions
r6_2.0_3.2	r6_functions
r6_2.0_3.3	r6_functions
r6_2.0_4.1	r6_functions
r6_2.1_1.5	r6_functions
r6_2.1_2.4	r6_functions
r6_2.1_3.0	r6_functions
r6_2.2_2.2	r6_functions
r6_2.2_2.3	r6_functions
r6_2.2_2.4	r6_functions
r6_2.2_3.2	r6_functions
r6_2.2_3.3	r6_functions
r6_2.3_2.3	r6_functions
r6_2.3_2.4	r6_functions
r6_2.3_3.2	r6_functions
r6_2.3_3.3	r6_functions
r6_2.4_2.4	r6_functions
r6_3.0_1.3	r6_functions
r6_3.0_1.4	r6_functions
r6_3.0_1.5	r6_functions
r6_3.0_2.2	r6_functions
r6_3.0_2.3	r6_functions
r6_3.0_2.4	r6_functions
r6_3.0_3.0	r6_functions
r6_3.0_3.1	r6_functions
r6_3.0_3.2	r6_functions
r6_3.0_3.3	r6_functions
r6_3.0_4.1	r6_functions
r6_3.3_2.4	r6_functions
r6_3.3_3.3	r6_functions
r6_functions	r6_functions
rightstr	rightstr
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_markers	screen_for_duplicate_markers
screen_for_NA_values	screen_for_NA_values
segregating_data	ALL_dosages
segtypeInfoSummary	segtypeInfoSummary
selSegtypeInfo	selSegtypeInfo
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
split_linkage_info	split_linkage_info
test_cluster_stack	test_cluster_stack
test_dosage_matrix	test_dosage_matrix
test_LG_hom_stack	test_LG_hom_stack
test_linkage_df	test_linkage_df
test_prefpairing	test_prefpairing
TRI_dosages	ALL_dosages
vector.to.matrix	vector.to.matrix
write.logheader	write.logheader
write.mct	write.mct
write.pwd	write.pwd
write.TSNPM	write.TSNPM
write_nested_list	write_nested_list
write_pwd_list	write_pwd_list
