# Linkage Analysis in Outcrossing Polyploids

## Documentation for package ‘polymapR’ version 1.0.19

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

polymapR-package | Linkage analysis in polyploids
add_dup_markers | Add back duplicate markers after mapping
ALL_dosages | A dosage matrix for a random pairing tetraploid with five linkage groups.
all_linkages_list_P1 | A (nested) list of linkage data frames classified per linkage group and homologue
all_linkages_list_P1_split | A (nested) list of linkage data frames classified per linkage group and homologue
all_linkages_list_P1_subset | A (nested) list of linkage data frames classified per linkage group and homologue
assembleDuplexLinks | Use bridge markers to cluster homologues into linkage groups
assign_linkage_group | Assign non-SN markers to a linkage group and homologue(s).
assign_SN_SN | Assign (leftover) 1.0 markers
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 using heatplots
check_marker_assignment | Check for consistent marker assignment between both parents
cluster_per_LG | Cluster 1.0 markers into correct homologues per linkage group
cluster_SN_markers | Cluster 1.0 markers
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
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
finish_linkage_analysis | Linkage analysis between all markertypes within LG.
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
LGHomDf_P1_1 | A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker
LGHomDf_P2_1 | A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker
LGHomDf_P2_2 | A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker
linkage | Calculate recombination frequency, LOD and phase
maplist_P1 | A list of maps of one parent
maplist_P1_subset | A list of maps of one parent
maplist_P2_subset | A list of maps of one parent
marker_assignments_P1 | A 'data.frame' with marker assignments
marker_assignments_P2 | A 'data.frame' with marker assignments
marker_binning | Perform binning of markers.
marker_binning_list | Bin markers that are in a nested list
marker_data_summary | Summarize marker data
MDSMap_from_list | Wrapper function for MDSMap to generate linkage maps from list of pairwise linkage estimates
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
P1_DxN_Assigned | A 'data.frame' with marker assignments
P1_homologues | A list of cluster stacks at different LOD scores
P1_SxS_Assigned | A 'data.frame' with marker assignments
P2_DxN_Assigned | A 'data.frame' with marker assignments
P2_homologues | A list of cluster stacks at different LOD scores
P2_homologues_triploid | A list of cluster stacks at different LOD scores
P2_SxS_Assigned | A 'data.frame' with marker assignments
P2_SxS_Assigned_2 | A 'data.frame' with marker assignments
p4_functions | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
parental_quantities | Calculate frequency of each markertype.
PCA_progeny | Perform a PCA on progeny
phased.maplist | A list of phased maps
phase_SN_diploid | Phase 1.0 markers at the diploid level
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
polymapR | Linkage analysis in polyploids
r2_1.0_1.0 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.
r2_1.0_1.1 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.
r2_1.1_1.1 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.
r2_functions | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.
r3_0.1_0.1 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_0.1_1.1 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_0.1_2.1 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
r3_2.1_2.1 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.
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
screened_data | A dosage matrix for a random pairing tetraploid with five linkage groups.
screened_data2 | A dosage matrix for a random pairing tetraploid with five linkage groups.
screened_data3 | A dosage matrix for a random pairing tetraploid with five linkage groups.
screen_for_duplicate_individuals | Screen for duplicate individuals
screen_for_duplicate_markers | Screen for and remove duplicated markers
screen_for_NA_values | Screen marker data for NA values
segregating_data | A dosage matrix for a random pairing tetraploid with five linkage groups.
SNSN_LOD_deviations | Identify deviations in LOD scores between pairs of simplex x nulliplex markers
SN_DN_P1 | A linkage 'data.frame'.
SN_DN_P2 | A linkage 'data.frame'.
SN_SN_P1 | A linkage 'data.frame'.
SN_SN_P2 | A linkage 'data.frame'.
SN_SN_P2_triploid | A linkage 'data.frame'.
SN_SS_P1 | A linkage 'data.frame'.
SN_SS_P2 | A linkage 'data.frame'.
split_linkage_info | Split linkage information into homologues
test_prefpairing | Check for and estimate preferential pairing
TRI_dosages | A dosage matrix for a random pairing tetraploid with five linkage groups.
write.mct | Write MapChart file
write.pwd | Write a JoinMap compatible .pwd file from linkage data.frame.
write.TSNPM | Write TetraploidSNPMap input file
write_nested_list | Write out a nested list
write_pwd_list | Write pwd files from a nested list