Revised Regression of Offspring on Mid-Parent (ROMPrev)

Software version 0.1 beta (October, 2006)

Overview

Testing for associations between polymorphisms and quantitative traits provides a tool that can help to identify the genetic effects underlying multifactorial disease. In addition to testing for association, the ability to estimate how much of the variation in a quantitative trait is attributable to variation at a given marker locus, i.e. the heritability attributable to the locus (or the locus-specific heritability), can help to assess the importance of a polymorphism found through association testing, and may help to prioritize subsequent studies. Locus-specific heritability can be used in a manner similar to the use of attributable risk in assessing what proportion of the disease in the population is attributable to a risk factor. This can be especially helpful in studying the etiology of multifactorial disease in which several loci and environmental factors are likely to play a role.

The Regression of Offspring on Mid-Parent (ROMP) method [Pugh et al. 2001; Roy-Gagnon 2004] is a test of association between a quantitative trait and a candidate locus. ROMP also estimates the trait heritability and the heritability attributable to a locus and requires genotyping offspring only. The revised version of the ROMP method (ROMPrev) [Roy-Gagnon et al. 2006] is implemented in this R suite of functions.

Features of the ROMPrev R suite

The suite includes functions to:

• Read in pedigree, phenotype, and SNP genotype data in a comma-delimited format and reformat the data for ROMPrev analysis (ROMPrevPrep function).
• Perform ROMPrev or ROOPrev analyses using parametric (ROMPrev and ROOPrev functions) or re-sampling (ROMPrevRS and ROOPrevRS functions) standard error and test of significance for the total and locus-specific heritability estimates. ROMPrev uses the mid-parent trait value while ROOPrev uses one parental value.
• Define nicely printed output (print.romp and print.romprs functions).

Download

Download each of the following files from this FTP site, and see the User's Guide for instructions:

ROMPrev_documentation.pdf

User's Guide

ROMPrev_v0.1.r

ROMPrev version 0.1 R functions

ROMPrev_example.r

Example code to call the functions

ROMPrev_example.data

Example data

ROMPrev_example.out

Example output

ROMPrev_example_out.csv

Example csv output

Please direct questions or comments about the ROMPrev software to Alexander F. Wilson, Ph D. (afw@mail.nih.gov).