CCAFE

CCAFE reconstructs case and control allele frequencies from summary statistics for genetic association studies.

Key Features:

• Summary Statistics-Based Reconstruction: Reconstructs case and control allele frequencies without requiring individual-level genotype data.
• Odds Ratio-Based Estimation: One function estimates allele frequencies using odds ratio (OR), number of cases (NCase), number of controls (NControl), and standard error of log odds ratio (SE(log(OR))).
• Whole Sample Allele Frequency-Based Estimation: A second function estimates allele frequencies using OR, NCase, NControl, and allele frequency for the whole sample (AF).

Scientific Applications:

• Case-Control Genetic Studies: Enables allele frequency estimation in cases and controls when only summary statistics are available from published genome-wide association studies.

Methodology:

CCAFE implements two computational functions for allele frequency reconstruction: one using OR, NCase, NControl, and SE(log(OR)); the second using OR, NCase, NControl, and AF for the whole sample.