# QTL Analysis in Autopolyploid Bi-Parental F1 Populations

## Documentation for package ‘polyqtlR’ version 0.0.9

- 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 | A data-frame of best linear unbiased predicted (BLUE) phenotypes (4x)
bx | Rcpp internal function Backward from forward-backward algorithm
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
fx | Rcpp internal function Forward from forward-backward algorithm
GIC_4x | A list of GIC estimates (4x)
hexa.list | A list of hexaploid bivalent pairing configurations
IBD_4x | A list of identity-by-descent probabilities (4x)
import_IBD | Import IBD probabilities as estimated by TetraOrigin
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 | A list of pairing predictions (4x)
phased_maplist.4x | A list of phased maps (4x)
Phenotypes_4x | A data-frame of phenotypes (4x)
plotLinearQTL | Plot the results of genome-wide QTL analysis along a single track
plotLinearQTL_list | Overlay the results of a number of genome-wide QTL analysis for which significance thresholds are available.
plotQTL | Plot the results of a previous QTL analysis
plotRecLS | Plot the recombination landscape across the genome
polyqtlR | QTL analysis in polyploid species using identity-by-descent probabilities
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 | A list of QTL results (4x)
Rec_Data_4x | A list of recombination count data (4x)
rem.hex | Redundant genotype classes in hexavalent transition matrix (6x)
rem.quad | Redundant genotype classes in quadrivalent transition matrix (4x)
segList_2x | A list of all possible bi-allelic QTL segregation types (2x)
segList_3x | A list of all possible bi-allelic QTL segregation types (3x)
segList_4x | A list of all possible bi-allelic QTL segregation types (4x)
segList_6x | A list of all possible bi-allelic QTL segregation types (6x)
segMaker | Create a list of possible QTL segregation types
singleMarkerRegression | Run a single marker regression using marker dosages
SNP_dosages.4x | A matrix of SNP marker dosages (4x)
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