cape-package |
Combinatorial Analysis of Epistasis and Pleiotropy |
calc.p |
Calculate P Values for Interactions Based on Permutations |
cape |
Combinatorial Analysis of Epistasis and Pleiotropy |
create.covar |
Designate a phenotype or treatment as a covariate |
delete.pheno |
Remove phenotypes from the phenotype matrix |
direct.influence |
Calculate the significance of direct influences of variant pairs on phenotypes |
error.prop |
Estimate Errors of Regression Coefficients |
get.covar |
Use a threshold to automatically select covariates for the pairscan |
get.eigentraits |
Calculate eigentraits from phenotype matrix |
get.network |
Convert the final results to a form plotted by 'plotNetwork' and 'plotCollapsedVarInf' |
norm.pheno |
Normalize and mean center phenotypes |
obesity.cross |
Mouse cross data from Reifsnyder et al. (2000) |
pairscan |
Perform regressions for all pairs of markers and all phenotypes. |
plotCollapsedVarInf |
Plot variant-to-variant influences |
plotNetwork |
Plot the final epistatic network |
plotPairscan |
plot the results from 'pairscan' |
plotSinglescan |
Plot the results of singlescan |
plotSVD |
Plot the results of the singular value decomposition of the phenotype matrix |
plotVariantInfluences |
Plot variant-to-variant influences |
read.population |
Read in and format data for analysis by 'cape' |
select.by.chr |
Subset a cross object to include only specified chromosomes. |
select.by.ind |
Subset a cross object to include specific individuals |
select.eigentraits |
Select a subset of the eigentraits for further analysis |
select.markers.for.pairscan |
A required step that filters variable and non-redundant markers for the pairscan |
select.pheno |
Select phenotypes for analysis |
set.covar |
Manually set which markers will be used as covariates. |
set.pairscan.thresh |
Manually set the threshold by which markers are selected for the pair scan |
singlescan |
Run the single-variant regression for all phenotypes |
writeVariantInfluences |
Write the final results to a file |