Cape-class              The CAPE data object
calc_delta_errors       Error propagation
calc_emp_p              Calculate empirical p-values
calc_p                  Calculate P Values for Interactions Based on
                        Permutations
cape2mpp                Converts a 'read_population' object to a
                        multi-parent object
direct_influence        Calculate the significance of direct influences
                        of variant pairs on phenotypes
error_prop              Estimate Errors of Regression Coefficients
get_covar               Get covariate information
get_eigentraits         Calculate eigentraits
get_geno                Gets the geno object
get_marker_location     Get marker genomic position
get_marker_name         Get marker names
get_network             Convert the final results to an adjacency
                        matrix.
get_pairs_for_pairscan
                        Select marker pairs for pairscan
get_pheno               Get the phenotype matrix
hist_pheno              Plot trait histograms
impute_missing_geno     Impute missing genotype data using k nearest
                        neighbors
kinship                 Calculate the kinship matrix
load_input_and_run_cape
                        Loads input and run CAPE
marker2covar            Creates a covariate from a genetic marker
norm_pheno              Mean-center and normalize phenotypes
pairscan                This function performs the pairwise scan on all
                        markers.
pheno2covar             Create a covariate from a trait
plink2cape              Convert plink2 files to cape format
plot_effects            Plot Interaction Effects
plot_full_network       Plot the final epistatic network in a
                        traditional network view.
plot_network            Plots cape results as a circular network
plot_pairscan           Plot the result of the pairwise scan
plot_pheno_cor          Plot trait pairs against each other
plot_singlescan         Plot results of single-locus scans
plot_svd                Plots eigentraits
plot_variant_influences
                        Plot cape coefficients
qnorm_pheno             Plot trait distributions
qtl2_to_cape            Convert qtl2 object to cape format
read_parameters         Read the parameter file, add missing entries
read_population         Reads in data in the R/qtl csv format
remove_ind              Remove individuals
remove_kin_ind          Removes individuals from the kinship object to
                        match the cape.obj
remove_markers          Removes genetic markers
remove_missing_genotype_data
                        Removes individuals and/or markers with missing
                        data
remove_unused_markers   Take out markers not used in cape
run_cape                Runs CAPE
select_eigentraits      Assign selected eigentraits in the Cape object
select_markers_for_pairscan
                        Select markers for the pairwise scan.
select_pheno            This function selects the phenotypes in a Cape
                        object
singlescan              Runs marker regression on each individual
                        genetic marker
write_population        Save the cross data in R/qtl CSV format
write_variant_influences
                        Write significant cape interactions to a csv
                        file
