# Linkage Analysis in Outcrossing Polyploids

## Documentation for package ‘polymapR’ version 1.1.6

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

## Help Pages

A B C D E F G H I L M O P R S T W

## -- A --

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

## -- B --

bridgeHomologues | Use bridge markers to cluster homologues into linkage groups

## -- C --

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_per_LG | Cluster 1.0 markers into correct homologues per linkage group
cluster_SN_markers | Cluster 1.0 markers
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

## -- D --

define_LG_structure | Generate linkage group and homologue structure of SxN markers

## -- E --

exampleRAD_mapping | Example output dataset of polyRAD::PipelineMapping2Parents function

## -- F --

finish_linkage_analysis | Linkage analysis between all markertypes within a linkage group.

## -- G --

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

## -- H --

homologue_lg_assignment | Assign markers to linkage groups and homologues.

## -- I --

integrated.maplist | A nested list with integrated maps

## -- L --

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
linkage.gp | Calculate recombination frequency, LOD and phase using genotype probabilities

## -- M --

map1 | A sample map
map2 | A sample map
map3 | A sample map
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_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
mout | Example output dataset of updog::multidog function

## -- O --

overviewSNlinks | Plotting 1.0 links between homologues

## -- P --

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_map | Plot linkage maps
plot_phased_maplist | Visualise the phased homologue maplist

## -- R --

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_2_1.0_1.0 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.
r3_2_1.0_1.1 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.
r3_2_1.0_1.2 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.
r3_2_1.2_1.2 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 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

## -- S --

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_individuals.gp | Screen for duplicate individuals using weighted genotype probabilities
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'.

## -- T --

test_prefpairing | Check for and estimate preferential pairing
TRI_dosages | A dosage matrix for a random pairing tetraploid with five linkage groups.

## -- W --

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