QTL Analysis in Autopolyploid Bi-Parental F1 Populations


[Up] [Top]

Documentation for package ‘polyqtlR’ version 0.0.5

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