| 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 |
| 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 |
| filter.hwe | Filter markers by Hardy-Weinberg equilibrium |
| filter.maf | Filter markers by minor allele frequency. |
| get.covar | Get information about covariates |
| get.eigentraits | Calculate eigentraits from phenotype matrix |
| get.geno | Retrieve the genotype matrix. |
| get.marker.chr | Get chromosome assignments for a vector of markers. |
| get.marker.idx | Get the column index of markers in the genotype matrix |
| get.marker.location | Get the chromosomal coordinate of markers |
| get.marker.name | Get marker names from marker numbers |
| get.marker.num | Get marker numbers from marker names |
| get.marker.val | Get marker values |
| get.network | Convert the final results to a form plotted by 'plotNetwork' and 'plotCollapsedVarInf' |
| get.pheno | Retrieve the genotype matrix. |
| histPheno | Plot histograms of phenotypes. |
| impute.missing.geno | Impute missing genotypes in measured markers. |
| make.data.obj | Generate data.obj from pheno.obj and geno.obj |
| marker2covar | Create a covariate from a genetic marker. |
| 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. |
| pheno2covar | Create a covariate from a phenotype. |
| plotCollapsedVarInf | Plot variant-to-variant influences |
| plotNetwork | Plot the final epistatic network |
| plotPairscan | plot the results from 'pairscan' |
| plotPheno | Plot phenotype values by individual. |
| plotPhenoCor | Plot correlations between phenotype pairs. |
| 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 |
| qqPheno | Plot qq plots of phenotype pairs. |
| read.geno | Read in and format data for analysis by 'cape' |
| read.pheno | Read in and format data for analysis by 'cape' |
| read.population | Read in and format data for analysis by 'cape' |
| remove.ind | Remove individuals from the data.obj |
| remove.markers | Remove markers from the data.obj |
| 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 |
| singlescan | Run the single-variant regression for all phenotypes |
| sortCross | Sort the genetic markers in the data.obj. |
| writePopulation | Write out a cape data object to .csv format. |
| writeVariantInfluences | Write the final results to a file |