# QTL Analysis in Autopolyploid Bi-Parental F1 Populations

## Documentation for package ‘polyqtlR’ version 0.1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

BLUE | Calculate Best Linear Unbiased Estimates using linear mixed model from 'nlme' package
BLUEs.pheno | Best Linear Unbiased Estimates of phenotype
check_cofactors | Build a multi-QTL model using step-wise procedure of checking genetic co-factors.
convert_mappoly_to_phased.maplist | Function to extract the phased map from a mappoly.map object
count_recombinations | Predict recombination breakpoints using IBD probabilities
estimate_GIC | Estimate the Genotypic Information Coefficient (GIC)
estimate_IBD | Generate IBD probabilities from marker genotypes and a phased linkage map
exploreQTL | Explore the possible segregation type of a QTL peak using Schwarz Information Criterion
findPeak | Function to find the position of maximum LOD on a particular linkage group
findSupport | Function to find a LOD - x support interval around a QTL position
GIC_4x | Genotypic Information Coefficient for example tetraploid
IBD_4x | Identical by descent probabilities for example tetraploid
import_IBD | Import IBD probabilities as estimated by TetraOrigin or PolyOrigin
impute_dosages | Re-estimate marker dosages given IBD input estimated using a high error prior.
maxL_IBD | Wrapper function to run estimate_IBD function over multiple error priors
meiosis_report | Generate a 'report' of predicted meiotic behaviour in an F1 population
mr.ls | Example output of meiosis report function
phased_maplist.4x | Phased maplist for example tetraploid
Phenotypes_4x | Phenotypes for example tetraploid
plotLinearQTL | Plot the results of QTL scan.
plotLinearQTL_list | Plot the results of QTL scan.
plotQTL | Plot the results of QTL scan.
plotRecLS | Plot the recombination landscape across the genome
PVE | Function to determine the percentage variance explained (PVE) of a (maximal) QTL model, and explore sub-models.
QTLscan | General QTL function that allows for co-factors, completely randomised block designs and the possibility to derive LOD thresholds using a permutation test
qtl_LODs.4x | QTL output for example tetraploid
Rec_Data_4x | Recombination data for example tetraploid
segList_2x | Expected segregation for all markers types of a diploid cross
segList_3x | Expected segregation for all markers types of a triploid cross (4 x 2)
segList_3x_24 | Expected segregation for all markers types of a triploid cross (2 x 4)
segList_4x | Expected segregation for all markers types of a tetraploid cross
segList_6x | Expected segregation for all markers types of a hexaploid cross
segMaker | Create a list of possible QTL segregation types
singleMarkerRegression | Run a single marker regression using marker dosages
SNP_dosages.4x | SNP marker dosage data for example tetraploid
spline_IBD | Fit splines to IBD probabilities
thinmap | Thin out map data
visualiseGIC | Visualise Genotypic Information Coefficient
visualiseHaplo | Visualise haplotypes in certain individuals in a certain region
visualisePairing | Visualise pairing of parental homologues
visualiseQTLeffects | Visualise QTL homologue effects around a QTL position