# QTL Analysis in Autopolyploid Bi-Parental F1 Populations

## Documentation for package ‘polyqtlR’ version 0.0.5

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

## Help Pages

bivTM | Bivalent transition matrix function
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
colour.bar | Add colour bar scale to heatplot
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
fast_IBD | Extremely fast estimation of identity-by-descent (IBD) probabilities.
fast_permute | Extension of the 'QTLscan' function, offering an optimised permutation test when the experimental setting (i.e. phenotype structure) is simple
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
hexTM | Hexavalent transition matrix function
hmm_IBD | Generate IBD probabilities from marker genotypes and a phased linkage map using HMM
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.
list.depth | Find depth of a list
mapseq | Generate a sequence of map positions for splining function
meiosis_report | Generate a 'report' of predicted meiotic behaviour in an F1 population
mr.ls | A list of pairing predictions (4x)
NettletonDoerge | Nettleton and Doerge 2000
Nstates.fun | Error handling on ploidy and ploidy2, and determine the number of genotype classes for general ploidy level and pairing behaviour
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
probgeno_df_to_array | Convert a progeno_df data.frame to a 3d array
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)
quadTM | Quadrivalent transition matrix function
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
state_fun | Function to return the list of possible pairing states, given parental ploidies and meiotic pairing model
test_dosage_matrix | Error and warning handling for dosage_matrix
test_IBD_list | Error and warning handling for IBD_list as estimated by 'estimate_IBD'
test_probgeno_df | Error and warning handling for probgeno_df data-frame of probabilistic genotypes (scores)
thinmap | Thin out map data
TM.biv.2 | Bivalent-pairing transition matrix function, diploid
TM.biv.4 | Bivalent-pairing transition matrix function, tetraploid
TM.biv.6 | Bivalent-pairing transition matrix function, hexaploid
TM.hex | Hexavalent-pairing transition matrix function, hexaploid
TM.quad | Quadrivalent-pairing transition matrix function, tetraploid
TMfun.2x_B | Diploid bi-parental transition matrix
TMfun.3x_BB | Triploid bi-parental transition matrix, bivalent-bivalent pairing
TMfun.3x_QB | Triploid bi-parental transition matrix, quadrivalent-bivalent pairing
TMfun.4x_BB | Tetraploid bi-parental transition matrix, bivalent-bivalent pairing
TMfun.4x_BQ | Tetraploid bi-parental transition matrix, bivalent-quadrivalent pairing
TMfun.4x_QB | Tetraploid bi-parental transition matrix, quadrivalent-bivalent pairing
TMfun.4x_QQ | Tetraploid bi-parental transition matrix, quadrivalent-quadrivalent pairing
TMfun.6x_BB | Hexaploid bi-parental transition matrix, bivalent-bivalent pairing
TMfun.6x_BH | Hexaploid bi-parental transition matrix, bivalent-hexavalent pairing
TMfun.6x_HB | Hexaploid bi-parental transition matrix, hexavalent-bivalent pairing
TMfun.6x_HH | Hexaploid bi-parental transition matrix, hexavalent-hexavalent pairing
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
weighted.var | Calculate the weighted variance
write.logheader | Write a header for the log file