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 |