calc.p                  Calculate P Values for Interactions Based on
                        Permutations
cape-package            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.
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
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
