Extract Information for Top Variant from Finemapping Results

This function extracts information about the variant with the highest Posterior Inclusion Probability (PIP) from finemapping results, typically used when no Credible Sets (CS) are identified in the analysis.

Usage

extract_top_pip_info(con_data)

Arguments

con_data

List. The method layer data from a finemapping RDS file.

Value

A data frame with one row containing the following columns:

cs_name

NA (as no CS is identified)

variants_per_cs

NA (as no CS is identified)

top_variant

ID of the variant with the highest PIP

top_variant_index

Index of the top variant in the original data

top_pip

Highest Posterior Inclusion Probability (PIP)

top_z

Z-score of the top variant

p_value

P-value calculated from the top Z-score

cs_corr

NA (as no CS correlation is available)

Details

This function is designed to be used when no Credible Sets are identified in the finemapping results, but information about the most significant variant is still desired. It identifies the variant with the highest PIP and extracts relevant statistical information.

Note

This function is particularly useful for capturing information about potentially important variants that might be included in Credible Sets under different analysis parameters or lower coverage. It maintains a structure similar to the output of `extract_cs_info()` for consistency in downstream analyses.

See also

extract_cs_info for processing when Credible Sets are present.