Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

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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