| 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 |
| plotSinglescan.heat | Plot the results of singlescan as a heatmap |
| 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 |
| writePopulation | Write out a cape data object to .csv format. |
| writeVariantInfluences | Write the final results to a file |