Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

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Documentation for package ‘cape’ version 3.1.0

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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