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
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 back duplicate markers after mapping
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
calcSegtypeInfo         Build a list of segregation types
checkF1                 Identify the best-fitting F1 segregation types
check_map               Check the quality of a linkage map
check_marker_assignment
                        Check for consistent marker assignment between
                        both parents
check_maxP              check your dataset's maxP distribution
chk1                    Example output of the checkF1 function
cluster_SN_markers      Cluster 1.0 markers
cluster_per_LG          Cluster 1.0 markers into correct homologues per
                        linkage group
compare_maps            Compare linkage maps, showing links between
                        connecting markers common to neighbouring maps
consensus_LG_assignment
                        Consensus LG assignment
consensus_LG_names      Find consensus linkage group names
convert_marker_dosages
                        Convert marker dosages to the basic types.
convert_polyRAD         Convert (probabilistic) genotype calling
                        results from polyRAD to input compatible with
                        polymapR
convert_updog           Convert (probabilistic) genotype calling
                        results from updog to input compatible with
                        polymapR.
correctDosages          Check if dosage scores may have to be shifted
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
exampleRAD_mapping      Example output dataset of
                        polyRAD::PipelineMapping2Parents function
finish_linkage_analysis
                        Linkage analysis between all markertypes within
                        a linkage group.
get_markertype_combinations
                        Visualize and get all markertype combinations
                        for which there are functions in polymapR
gp_df                   An example of a genotype probability data frame
gp_overview             gp_overview
gp_vignette_data        A list of objects needed to build the
                        probabilistic genotype vignette
homologue_lg_assignment
                        Assign markers to linkage groups and
                        homologues.
integrated.maplist      A nested list with integrated maps
linkage                 Calculate recombination frequency, LOD and
                        phase
linkage.gp              Calculate recombination frequency, LOD and
                        phase using genotype probabilities
map1                    A sample map
map2                    A sample map
map3                    A sample map
maplist_P1              A list of maps of one parent
marker_binning          Perform binning of markers.
marker_data_summary     Summarize marker data
merge_homologues        Merge homologues
mout                    Example output dataset of updog::multidog
                        function
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_hom_vs_LG          Plot homologue position versus integrated
                        positions
plot_map                Plot linkage maps
plot_phased_maplist     Visualise the phased homologue maplist
r2_functions            Calculate recombination frequency, LOD and
                        log-likelihood from frequency tables in a
                        random pairing diploid cross.
r3_functions            Calculate recombination frequency, LOD and
                        log-likelihood from frequency tables in a
                        random pairing triploid from a 4x2 or 2x4
                        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
screen_for_NA_values    Screen marker data for NA values
screen_for_duplicate_individuals
                        Screen for duplicate individuals
screen_for_duplicate_individuals.gp
                        Screen for duplicate individuals using weighted
                        genotype probabilities
screen_for_duplicate_markers
                        Screen for and remove duplicated markers
test_prefpairing        Check for and estimate preferential pairing
write.TSNPM             Write TetraploidSNPMap input 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
