HAPFAM :: Haplotype Association Analysis of Quantitative Traits in Family Studies

HAPFAM is a computer program for the efficient haplotype association analysis of quantitative traits in family studies, as described in Diao and Lin (2013, submitted).

General Information

The program is written in C language. Executable file for Linux/Mac platform is available in the download section below.

Usage

On Linux systems:

hapfam_linux control_parameter_input_file_name

On Mac systems:

hapfam_mac control_parameter_input_file_name

Input

The program requires two separate groups of input: the control parameter input and the data input.

The genotype data input file is a plain text file with n rows and 6+2d columns, where d is the number of SNPs. The rows represent subjects. The columns are separated by one or more white spaces (the space character or the TAB character). The columns have fixed meanings, as described below:

Column 1: Pedigree ID
Column 2: Subject ID
Column 3: Father ID
Column 4: Mother ID
Column 5: Gender
Column 6: Indicator of homozygous twins
Column 7 – column 6+2d: Genotype data for SNPs #1 - #d

The phenotype data input file is a plain text file with n rows and 2+p columns, where p is total number of quantitative traits. The rows represent subjects. The columns are separated by one or more white spaces (the space character or the TAB character). The columns have fixed meanings, as described below:

Column 1: Pedigree ID
Column 2: Subject ID
Column 3 – column 2+p: Phenotypes #1 - #p

The control parameters input file contains the file names of genotype and phenotype data input files, total number of subjects, total number of SNPs, total number of phenotypes, and the index number of the phenotype of interest. The rows have fixed meaning, as described below:

Row 1: File name of genotype data input. Character.
Row 2: Total number of subjects. Integer.
Row 3: Total number of SNPs. Integer.
Row 4: File name of phenotype data input. Character.
Row 5: Total number of subjects. Integer.
Row 6: Total number of phenotypes. Character.
Row 7: Index number of phenotype of interest. Integer.

Output

Computational results include the estimates of the haplotype frequencies, inbreeding coefficient, and their corresponding standard error estimates. In addition, the results include the likelihood ratio test statistics for testing the haplotype effects for the six most frequent haplotypes.

Example

The file test_ped.dat and test_phe.dat contains a simulated data set with 200 nuclear families, each with two parents and one offspring. The control parameters are given in test.inf. The output file is test.out.

Download

» hapfam_linx

» hapfam_mac