QTL Analysis in Autopolyploid Bi-Parental F1 Populations

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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