# Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

## Documentation for package ‘cape’ version 3.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

calc_delta_errors | Error propagation
calc_emp_p | Calculate empirical p-values
calc_p | Calculate P Values for Interactions Based on Permutations
Cape | The CAPE data object
Cape-class | The CAPE data object
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