ALL_dosages             A dosage matrix for a random pairing tetraploid
                        with five linkage groups.
LGHomDf_P1_1            A 'data.frame' specifying the assigned
                        homologue and linkage group number per SxN
                        marker
MDSMap_from_list        Wrapper function for MDSMap to generate linkage
                        maps from list of pairwise linkage estimates
Mode                    Calculate the mode of a vector
P1_SxS_Assigned         A 'data.frame' with marker assignments
P1_homologues           A list of cluster stacks at different LOD
                        scores
PCA_progeny             Perform a PCA on progeny
SNSN_LOD_deviations     Identify deviations in LOD scores between pairs
                        of simplex x nulliplex markers
SN_SN_P1                A linkage 'data.frame'.
add_dup_markers         Add duplicate markers to a map
all_linkages_list_P1    A (nested) list of linkage data frames
                        classified per linkage group and homologue
assign_SN_SN            Assign (leftover) 1.0 markers
assign_linkage_group    Assign non-SN markers to a linkage group and
                        homologue(s).
bridgeHomologues        Use bridge markers to cluster homologues into
                        linkage groups
calcPotShifts           Calculate potential shifts in marker dosages
calcSegtypeInfo         Build a list of segregation types
calc_binning_thresholds
                        calc_binning_thresholds
calc_q1                 calc_q1
                        ***********************************************************
calc_q2                 calc_q2
                        ***********************************************************
calc_q3                 calc_q3
                        ***********************************************************
calc_qall               calc_qall
                        ***********************************************************
checkF1                 Identify the best-fitting F1 segregation types
checkFilename           checkFilename
                        ***********************************************************
check_map               Check the quality of a linkage map using
                        heatplots
check_marker_assignment
                        Check for consistent marker assignment between
                        both parents
chk2integer             chk2integer
                        ***********************************************************
cluster_SN_markers      Cluster 1.0 markers
cluster_per_LG          Cluster 1.0 markers into correct homologues per
                        linkage group
colour.bar              Add colour bar scale to heatplot
consensus_LG_assignment
                        Consensus LG assignment
consensus_LG_names      Find consensus linkage group names
convert_marker_dosages
                        Convert marker dosages to the basic types.
correctDosages          Check if dosage scores may have to be shifted
createChmHomList        User interface for specifying linkage group for
                        a homologue
createMap               Marker ordering function
createTetraOriginInput
                        Create input files for TetraOrigin using an
                        integrated linkage map list and marker dosage
                        matrix
create_phased_maplist   Create a phased homologue map list using the
                        original dosages
define_LG_structure     Generate linkage group and homologue structure
                        of SxN markers
digamfrq                digamfrq
                        ***********************************************************
finish_linkage_analysis
                        Linkage analysis between all markertypes within
                        LG.
gcd                     gcd
                        ***********************************************************
gcd_all                 gcd_all
                        ***********************************************************
getConsensusGeno        getConsensusGeno
                        ***********************************************************
getMatchParents         getMatchParents
                        ***********************************************************
get_markertype_combinations
                        Visualize and get all markertype combinations
                        for which there are functions in polymapR
homologue_lg_assignment
                        Assign markers to linkage groups and
                        homologues.
integrated.maplist      A nested list with integrated maps
leftstr                 Get substrings from the lefthand side
linkage                 Calculate recombination frequency, LOD and
                        phase
linterpol               linterpol
                        ***********************************************************
makeProgeny             makeProgeny
                        ***********************************************************
maplist_P1              A list of maps of one parent
marker_binning          Perform binning of markers.
marker_binning_list     Bin markers that are in a nested list
marker_data_summary     Summarize marker data
merge_homologues        Merge homologues
merge_marker_assignments
                        Merge marker assignments
orient_and_merge_maps   Align and integrate maps
overviewSNlinks         Plotting 1.0 links between homologues
p4_functions            Calculate recombination frequency, LOD and
                        log-likelihood from frequency tables in a
                        preferential pairing tetraploid
parental_quantities     Calculate frequency of each markertype.
phase_SN_diploid        Phase 1.0 markers at the diploid level
phased.maplist          A list of phased maps
plot_SNlinks            Plot links between 1.0 markers
plot_hom_vs_LG          Plot homologue position versus integrated
                        positions
plot_linkage_df         Plot r versus LOD grouped by phase
plot_map                Plot linkage maps
plot_phased_maplist     Visualise the phased homologue maplist
polygamfrq              polygamfrq
                        ***********************************************************
polymapR                Linkage analysis in polyploids
prepare_pwd             Prepare pwd for mapping scripts e.g. MDSmap
r3_functions            Calculate recombination frequency, LOD and
                        log-likelihood from frequency tables in a
                        random pairing triploid from a tetraploid x
                        diploid cross.
r4_functions            Calculate recombination frequency, LOD and
                        log-likelihood from frequency tables in a
                        random pairing tetraploid
r6_functions            Calculate recombination frequency, LOD and
                        log-likelihood from frequency tables in a
                        random pairing hexaploid
r_LOD_plot              Plot r versus LOD
rightstr                Get substrings from the righthand side
screen_for_NA_values    Screen marker data for NA values
screen_for_duplicate_individuals
                        Screen for duplicate individuals
screen_for_duplicate_markers
                        Screen for and remove duplicated markers
segtypeInfoSummary      Summarize the segtypeInfo list
selSegtypeInfo          Restrict a list of segregation types to
                        specified inheritance modes
split_linkage_info      Split linkage information into homologues
test_LG_hom_stack       Error and warning handling for LG_hom_stack
test_cluster_stack      Error and warning handling for cluster_stack
test_dosage_matrix      Error and warning handling for dosage_matrix
test_linkage_df         Error and warning handling for linkage_df
test_prefpairing        Check for and estimate preferential pairing
vector.to.matrix        Large vector or in standardized matrix
write.TSNPM             Write TetraploidSNPMap input file
write.logheader         Write a header for the log file
write.mct               Write MapChart file
write.pwd               Write a JoinMap compatible .pwd file from
                        linkage data.frame.
write_nested_list       Write out a nested list
write_pwd_list          Write pwd files from a nested list
