Learn R Programming

polymapR (version 1.1.5)

Linkage Analysis in Outcrossing Polyploids

Description

Creation of linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) . Since version 1.1.0, both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) .

Copy Link

Version

Install

install.packages('polymapR')

Monthly Downloads

630

Version

1.1.5

License

GPL

Maintainer

Peter Bourke

Last Published

January 8th, 2024

Functions in polymapR (1.1.5)

chk1

Example output of the checkF1 function
cluster_SN_markers

Cluster 1.0 markers
assign_linkage_group

Assign non-SN markers to a linkage group and homologue(s).
check_marker_assignment

Check for consistent marker assignment between both parents
calcSegtypeInfo

Build a list of segregation types
check_map

Check the quality of a linkage map using heatplots
checkF1

Identify the best-fitting F1 segregation types
check_maxP

check your dataset's maxP distribution
bridgeHomologues

Use bridge markers to cluster homologues into linkage groups
assign_SN_SN

Assign (leftover) 1.0 markers
convert_updog

Convert (probabilistic) genotype calling results from updog to input compatible with polymapR.
cluster_per_LG

Cluster 1.0 markers into correct homologues per linkage group
correctDosages

Check if dosage scores may have to be shifted
compare_maps

Compare linkage maps, showing links between connecting markers common to neighbouring maps
convert_marker_dosages

Convert marker dosages to the basic types.
createTetraOriginInput

Create input files for TetraOrigin using an integrated linkage map list and marker dosage matrix
consensus_LG_assignment

Consensus LG assignment
create_phased_maplist

Create a phased homologue map list using the original dosages
consensus_LG_names

Find consensus linkage group names
convert_polyRAD

Convert (probabilistic) genotype calling results from polyRAD to input compatible with polymapR
define_LG_structure

Generate linkage group and homologue structure of SxN markers
get_markertype_combinations

Visualize and get all markertype combinations for which there are functions in polymapR
linkage

Calculate recombination frequency, LOD and phase
exampleRAD_mapping

Example output dataset of polyRAD::PipelineMapping2Parents function
homologue_lg_assignment

Assign markers to linkage groups and homologues.
gp_overview

gp_overview
finish_linkage_analysis

Linkage analysis between all markertypes within a linkage group.
marker_binning

Perform binning of markers.
integrated.maplist

A nested list with integrated maps
overviewSNlinks

Plotting 1.0 links between homologues
linkage.gp

Calculate recombination frequency, LOD and phase using genotype probabilities
gp_vignette_data

A list of objects needed to build the probabilistic genotype vignette
gp_df

An example of a genotype probability data frame
map3

A sample map
plot_phased_maplist

Visualise the phased homologue maplist
marker_data_summary

Summarize marker data
merge_homologues

Merge homologues
r2_functions

Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.
phased.maplist

A list of phased maps
map2

A sample map
maplist_P1

A list of maps of one parent
map1

A sample map
mout

Example output dataset of updog::multidog function
plot_map

Plot linkage maps
phase_SN_diploid

Phase 1.0 markers at the diploid level
parental_quantities

Calculate frequency of each markertype.
p4_functions

Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid
plot_hom_vs_LG

Plot homologue position versus integrated positions
r3_functions

Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.
polymapR-package

polymapR: Linkage Analysis in Outcrossing Polyploids
r6_functions

Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid
screen_for_duplicate_markers

Screen for and remove duplicated markers
write.TSNPM

Write TetraploidSNPMap input file
r_LOD_plot

Plot r versus LOD
test_prefpairing

Check for and estimate preferential pairing
r4_functions

Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid
screen_for_NA_values

Screen marker data for NA values
screen_for_duplicate_individuals.gp

Screen for duplicate individuals using weighted genotype probabilities
write.mct

Write MapChart file
screen_for_duplicate_individuals

Screen for duplicate individuals
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
SNSN_LOD_deviations

Identify deviations in LOD scores between pairs of simplex x nulliplex markers
MDSMap_from_list

Wrapper function for MDSMap to generate linkage maps from list of pairwise linkage estimates
ALL_dosages

A dosage matrix for a random pairing tetraploid with five linkage groups.
PCA_progeny

Perform a PCA on progeny
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
P1_SxS_Assigned

A data.frame with marker assignments
P1_homologues

A list of cluster stacks at different LOD scores
LGHomDf_P1_1

A data.frame specifying the assigned homologue and linkage group number per SxN marker
SN_SN_P1

A linkage data.frame.