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polymapR (version 1.0.20)

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) .

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Version

Install

install.packages('polymapR')

Monthly Downloads

739

Version

1.0.20

License

GPL

Maintainer

Peter Bourke

Last Published

December 12th, 2019

Functions in polymapR (1.0.20)

define_LG_structure

Generate linkage group and homologue structure of SxN markers

consensus_LG_assignment

Consensus LG assignment

finish_linkage_analysis

Linkage analysis between all markertypes within LG.

merge_homologues

Merge homologues

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

orient_and_merge_maps

Align and integrate maps

marker_data_summary

Summarize marker data

merge_marker_assignments

Merge marker assignments

check_marker_assignment

Check for consistent marker assignment between both parents

cluster_SN_markers

Cluster 1.0 markers

convert_marker_dosages

Convert marker dosages to the basic types.

consensus_LG_names

Find consensus linkage group names

integrated.maplist

A nested list with integrated maps

A list of cluster stacks at different LOD scores

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

Linkage analysis in polyploids

plot_phased_maplist

Visualise the phased homologue maplist

Check if dosage scores may have to be shifted

overviewSNlinks

Plotting 1.0 links between homologues

Write pwd files from a nested list

A list of maps of one parent

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

add_dup_markers

Add back duplicate markers after mapping

Calculate recombination frequency, LOD and phase

Perform a PCA on progeny

Write MapChart file

Write TetraploidSNPMap input file

Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a tetraploid x diploid cross.

A list of phased maps

all_linkages_list_P1

A (nested) list of linkage data frames classified per linkage group and homologue

Plot homologue position versus integrated positions

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

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

calcSegtypeInfo

Build a list of segregation types

homologue_lg_assignment

Assign markers to linkage groups and homologues.

get_markertype_combinations

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

bridgeHomologues

Use bridge markers to cluster homologues into linkage groups

split_linkage_info

Split linkage information into homologues

test_prefpairing

Check for and estimate preferential pairing

Assign (leftover) 1.0 markers

plot_linkage_df

Plot r versus LOD grouped by phase

Perform binning of markers.

Plot linkage maps

marker_binning_list

Bin markers that are in a nested list

Plot r versus LOD

screen_for_NA_values

Screen marker data for NA values

phase_SN_diploid

Phase 1.0 markers at the diploid level

assign_linkage_group

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

parental_quantities

Calculate frequency of each markertype.

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

screen_for_duplicate_individuals

Screen for duplicate individuals

write_nested_list

Write out a nested list

Write a JoinMap compatible .pwd file from linkage data.frame.

screen_for_duplicate_markers

Screen for and remove duplicated markers

MDSMap_from_list

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

Cluster 1.0 markers into correct homologues per linkage group

P1_SxS_Assigned

A data.frame with marker assignments

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

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

SNSN_LOD_deviations

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

A linkage data.frame.

Identify the best-fitting F1 segregation types

Check the quality of a linkage map using heatplots