FAME

This is the software for FAst Marginal Epistasis test (FAME)

link: [https://www.biorxiv.org/content/10.1101/2023.09.10.557084v1.abstract]

Prerequisites

The following packages are required on a Linux machine to compile and use the software package.

g++
cmakes
make

General description

Given a genotype matrix (NxM) encoded as plink format (bim, fam, bed), the target trait in the same format, and an annotation file (MxK) with K bins across the M features, FAME jointly estimates the marginal effect across all the SNPs and the ME effect of the target SNP at k-th bin.

Note:

Intuitively, an annotation file guides the software on how to partition the genotype matrix by features. The column number of the annotation file determines the number of partitions made to the feature space. One basic rule of creating the annotation file: each row should contain one and only one "1", and all the rest columns of the same row should be 0s.

To run the code, please delete the existing build folder (if any) and then use the following commands to compile the executable code.

mkdir build
cd build
cmake ..
make

Parameters

GENIE_GXG:
-g: path to genotype
-p: path to phenotype
-gxgbin: the bin index to compute the ME effect (0-based)
-snp: the target SNP index (1-based)
-k: number of random vector
-jn: number of jackknife blocks
-o: output file
-annot: annotation file

Two examples have been provided in the path example.

• To test FAME with single bin:

  cd example/single-bin
  sh test.sh

• To test FAME with multiple bins:

  cd example/multi-bin
  sh test.sh

Output:

K+2 estimated variance components will be reported. The first K components correspond to the additive component at each bin; the K+1 th component corresponds to the ME effect of the target bin; and the K+2 th component corresponds to the i.i.d. noise component.