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Process Credible Sets (CS) from Finemapping Results

Source: R/univariate_rss_diagnostics.R
extract_cs_info.Rd

This function extracts and processes information for each Credible Set (CS) from finemapping results, typically obtained from a finemapping RDS file.

Usage

extract_cs_info(con_data, cs_names, top_loci_table)

Arguments

con_data

List. The method layer data from a finemapping RDS file that is not empty.

cs_names

Character vector. Names of the Credible Sets, usually in the format "L_<number>".

top_loci_table

Data frame. The $top_loci layer data from the finemapping results.

Value

A data frame with one row per CS, containing the following columns:

cs_name

Name of the Credible Set

variants_per_cs

Number of variants in the CS

top_variant

ID of the variant with the highest PIP in the CS

top_variant_index

Global index of the top variant

top_pip

Highest Posterior Inclusion Probability (PIP) in the CS

top_z

Z-score of the top variant

p_value

P-value calculated from the top Z-score

cs_corr

Pairwise correlations of other CSs in this RDS with the CS of the current row, delimited by '|', if there is more than one CS in this RDS file

Details

This function is designed to be used only when there is at least one Credible Set in the finemapping results usually for a given study and block. It processes each CS, extracting key information such as the top variant, its statistics, and correlation information between multiple CS if available.