Linkage Analysis in Outcrossing Polyploids
Use bridge markers to cluster homologues into linkage groups
Build a list of segregation types
Convert (probabilistic) genotype calling results from polyRAD to input...
Assign markers to linkage groups and homologues.
Calculate recombination frequency, LOD and phase using genotype probab...
Calculate recombination frequency, LOD and phase
Visualise the phased homologue maplist
Assign (leftover) 1.0 markers
Add back duplicate markers after mapping
Assign non-SN markers to a linkage group and homologue(s).
Check the quality of a linkage map
Check for consistent marker assignment between both parents
check your dataset's maxP distribution
Identify the best-fitting F1 segregation types
Cluster 1.0 markers into correct homologues per linkage group
Cluster 1.0 markers
Compare linkage maps, showing links between connecting markers common ...
Consensus LG assignment
Find consensus linkage group names
Convert marker dosages to the basic types.
Convert (probabilistic) genotype calling results from updog to input c...
Check if dosage scores may have to be shifted
Create a phased homologue map list using the original dosages
Create input files for TetraOrigin using an integrated linkage map lis...
Generate linkage group and homologue structure of SxN markers
Linkage analysis between all markertypes within a linkage group.
Visualize and get all markertype combinations for which there are func...
gp_overview
Perform binning of markers.
Summarize marker data
Wrapper function for MDSMap to generate linkage maps from list of pair...
Merge homologues
Plotting 1.0 links between homologues
Calculate recombination frequency, LOD and log-likelihood from frequen...
Calculate frequency of each markertype.
Perform a PCA on progeny
Phase 1.0 markers at the diploid level
Plot homologue position versus integrated positions
Plot linkage maps
polymapR: Linkage Analysis in Outcrossing Polyploids
Plot r versus LOD
Calculate recombination frequency, LOD and log-likelihood from frequen...
Calculate recombination frequency, LOD and log-likelihood from frequen...
Calculate recombination frequency, LOD and log-likelihood from frequen...
Calculate recombination frequency, LOD and log-likelihood from frequen...
Screen for duplicate individuals using weighted genotype probabilities
Screen for duplicate individuals
Screen for and remove duplicated markers
Screen marker data for NA values
Identify deviations in LOD scores between pairs of simplex x nulliplex...
Check for and estimate preferential pairing
Write MapChart file
Write a JoinMap compatible .pwd file from linkage data.frame.
Write TetraploidSNPMap input file
Write out a nested list
Write pwd files from a nested list
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) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0, both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) <doi:10.1007/s00122-021-03834-x>.