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 |