QTL Analysis in Autopolyploid Bi-Parental F1 Populations

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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