Identifying Trait-Relevant Functional Annotations


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Documentation for package ‘rolypoly’ version 0.1.0

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rolypoly-package The rolypoly package for identifying annotations associated with complex traits.
bootstrap_estimator Bootstrap parameter estimates for confidence intervals.
calculate_annotation_block_heritability Caclulate the contribution of block annotations to the heritability of a trait.
calculate_block_values Caclulate predicted block values based on block information and model fit.
calculate_expected_block_values_given_ld Caclulate predicted block values based on block information and model fit.
cv_regularized_parameter_estimator Perform regularization inference.
data_io Functions for opening and organizing data.
inference Inference functions.
main_wrapper Main wrapper functions.
make_ld_matrix Helper function to pull LD data from NCBI.
make_results_df Helper function to make a summary table of results from bootstrap data.
parameter_estimator Find parameter estimates for the data.
plot_rolypoly_annotation_estimates Visualize parameter estimates after running inference
plot_rolypoly_annotation_ranking Rank annotations by p-value after running inference
regularized_inference Inference functions that include regularization
robust_parameter_estimator Find robust parameter estimates for the data.
rolypoly The rolypoly package for identifying annotations associated with complex traits.
rolypoly_add_ld_corrected_gwas_block_scores Add LD corrected block scores to rolypoly.
rolypoly_link_blocks_and_gwas Link blocks and gwas
rolypoly_load_block_annotation Load annotations for blocks of LD, in some cases this is a gene annotation with a window around a gene.
rolypoly_load_block_data Block annotations, usually gene model.
rolypoly_load_gwas Load gwas data
rolypoly_perform_inference Run inference.
rolypoly_perform_regularized_inference Run inference with added regularization.
rolypoly_plots Plot functions.
rolypoly_roll Main rolypoly wrapper function.
sim_block_annotation Simulated block data annotation.
sim_expression_data_normalized Simulated expression data.
sim_gwas_data Simulated GWAS summary statistics
vectorize_rolypoly Take a list of rolypoly data and vectorize it for inference.