QTL Analysis in Autopolyploid Bi-Parental F1 Populations
Calculate Best Linear Unbiased Estimates using linear mixed model from...
Build a multi-QTL model using step-wise procedure of checking genetic ...
Function to extract the phased map from a mappoly.map object
Predict recombination breakpoints using IBD probabilities
Estimate the Genotypic Information Coefficient (GIC)
Generate IBD probabilities from marker genotypes and a phased linkage ...
Explore the possible segregation type of a QTL peak using Schwarz Info...
Function to find the position of maximum LOD on a particular linkage g...
Function to find a LOD - x support interval around a QTL position
Import IBD probabilities as estimated by TetraOrigin or PolyOrigin
Re-estimate marker dosages given IBD input estimated using a high erro...
Wrapper function to run estimate_IBD function over multiple error prio...
Generate a 'report' of predicted meiotic behaviour in an F1 population
Plot the results of QTL scan.
Plot the recombination landscape across the genome
QTL analysis in polyploid species using posterior genotype probabiliti...
Function to determine the percentage variance explained (PVE) of a (ma...
General QTL function that allows for co-factors, completely randomised...
Create a list of possible QTL segregation types
Run a single marker regression using marker dosages
Fit splines to IBD probabilities
Thin out map data
Visualise Genotypic Information Coefficient
Visualise haplotypes in certain individuals in a certain region
Visualise pairing of parental homologues
Visualise QTL homologue effects around a QTL position
Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in autopolyploid bi-parental F1 populations. For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated. Significance thresholds, exploring QTL allele effects and visualising results are provided. For more background and to reference the package see <doi:10.1093/bioinformatics/btab574>.