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polymapR (version 1.0.17)

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 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

1.0.17

License

GPL

Maintainer

Peter Bourke

Last Published

August 24th, 2018

Functions in polymapR (1.0.17)

Calculate potential shifts in marker dosages

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

segtypeInfoSummary

Summarize the segtypeInfo list

Plot links between 1.0 markers

calc_q2 ***********************************************************

finish_linkage_analysis

Linkage analysis between all markertypes within LG.

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

cluster_SN_markers

Cluster 1.0 markers

makeProgeny ***********************************************************

check_marker_assignment

Check for consistent marker assignment between both parents

linterpol ***********************************************************

MDSMap_from_list

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

marker_data_summary

Summarize marker data

consensus_LG_assignment

Consensus LG assignment

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

test_prefpairing

Check for and estimate preferential pairing

Calculate the mode of a vector

assign_linkage_group

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

calcSegtypeInfo

Build a list of segregation types

calc_binning_thresholds

calc_binning_thresholds

test_LG_hom_stack

Error and warning handling for LG_hom_stack

Check if dosage scores may have to be shifted

Assign (leftover) 1.0 markers

write.logheader

Write a header for the log file

A linkage data.frame.

add_dup_markers

Add back duplicate markers after mapping

calc_q3 ***********************************************************

Plot r versus LOD

phase_SN_diploid

Phase 1.0 markers at the diploid level

Add colour bar scale to heatplot

gcd ***********************************************************

digamfrq ***********************************************************

bridgeHomologues

Use bridge markers to cluster homologues into linkage groups

plot_phased_maplist

Visualise the phased homologue maplist

Perform a PCA on progeny

orient_and_merge_maps

Align and integrate maps

Get substrings from the lefthand side

Plot homologue position versus integrated positions

SNSN_LOD_deviations

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

polygamfrq ***********************************************************

Write TetraploidSNPMap input file

P1_SxS_Assigned

A data.frame with marker assignments

Write MapChart file

getMatchParents

getMatchParents ***********************************************************

A list of cluster stacks at different LOD scores

consensus_LG_names

Find consensus linkage group names

convert_marker_dosages

Convert marker dosages to the basic types.

integrated.maplist

A nested list with integrated maps

checkFilename ***********************************************************

calc_q1 ***********************************************************

A list of maps of one parent

Check the quality of a linkage map using heatplots

Restrict a list of segregation types to specified inheritance modes

Prepare pwd for mapping scripts e.g. MDSmap

create_phased_maplist

Create a phased homologue map list using the original dosages

Linkage analysis in polyploids

parental_quantities

Calculate frequency of each markertype.

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

Get substrings from the righthand side

Identify the best-fitting F1 segregation types

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

createChmHomList

User interface for specifying linkage group for a homologue

getConsensusGeno

getConsensusGeno ***********************************************************

Marker ordering function

createTetraOriginInput

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

Calculate recombination frequency, LOD and phase

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

homologue_lg_assignment

Assign markers to linkage groups and homologues.

merge_marker_assignments

Merge marker assignments

all_linkages_list_P1

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

merge_homologues

Merge homologues

test_linkage_df

Error and warning handling for linkage_df

test_dosage_matrix

Error and warning handling for dosage_matrix

overviewSNlinks

Plotting 1.0 links between homologues

plot_linkage_df

Plot r versus LOD grouped by phase

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

Plot linkage maps

screen_for_duplicate_markers

Screen for and remove duplicated markers

calc_qall ***********************************************************

vector.to.matrix

Large vector or in standardized matrix

A list of phased maps

split_linkage_info

Split linkage information into homologues

gcd_all ***********************************************************

Perform binning of markers.

marker_binning_list

Bin markers that are in a nested list

test_cluster_stack

Error and warning handling for cluster_stack

write_nested_list

Write out a nested list

screen_for_NA_values

Screen marker data for NA values

screen_for_duplicate_individuals

Screen for duplicate individuals

Write pwd files from a nested list

Cluster 1.0 markers into correct homologues per linkage group

chk2integer ***********************************************************