calc.p                  Calculate P Values for Interactions Based on
                        Permutations
cape-package            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'
plotSVD                 Plot the results of the singular value
                        decomposition of the phenotype matrix
plotSinglescan          Plot the results of singlescan
plotSinglescan.heat     Plot the results of singlescan as a heatmap
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
