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 |