Q-ROADTRIPS (beta) 1.0 is a C program that performs single-SNP, quantitative trait association testing in samples with partially or completely unknown population and/or pedigree structure. Q-ROADTRIPS is an extension of the ROADTRIPS case-control method to quantitative traits: Thornton T., McPeek M. S. "ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure" (2010) American Journal of Human Genetics, vol 86, pp. 172-184. Q-ROADTRIPS uses an empirical covariance matrix calculated from genomewide SNP data to correct for unknown population and pedigree structure.
Q- ROADTRIPS is suitable for applications such as correcting for partially or completely un-known population structure and/or relatedness in the context of GWAS. The Q-ROADTRIPS program can be used for the analysis of any quantitative trait and there are no restrictions on the types of distributions allowed. For example, a trait can follow a normal distribution, can be count values (e.g., from a poisson distribution), a mixture of different distributions, or the distribution of the trait can be completely unknown. Analysis can be performed genomewide (currently just for autosomes).
The current version of Q-ROADTRIPS is (beta) release 1.0. Q-ROADTRIPS support PLINK's transposed PED file.
Instructions
1. Use PLINK software to transpose your genotype files (bed or ped format) to tped/tfam format by running
% plink --bfile [bed_prefix] (or --file [ped_prefix]) --recode12 --output-missing-genotype 0 --transpose --out [tped_prefix]
2. Reformat the phenotype files in the same order of .tfam files. The phenotype file has six entries at each line in the following order: Family ID, Individual ID, Father ID, Mother ID, Sex, and Phenotype. Farther ID, Mother ID, and Sex values will be ignored by the program, however, some string must be present for these columns. Missing phenotype values should be represented as "NA". We recommend using phenotypes that have been adjusted for any relevant covariants, e.g., regress out covariates for the phenotypes.
Sample lines of phenotype files. (tab or space delimited)
59811 8598110 0 0 2 0.0735 862311 862311 0 0 2 1.309 864111 864111 0 0 1 -1.54 865211 865211 0 0 1 0.23982 875511 875511 0 0 2 NA 880111 880111 0 0 1 0.1148 880811 880811 0 0 2 0.423 881511 881511 0 0 2 -1.123 88211 88211 0 0 5 2.456
3. To run Q-ROADTRIPS with a PLINK tped file named "myfile.tped" and phenotype file named "myfile.pheno", the following commands can be used.
% QROADTRIPS -g myfile.tped -p myfile.pheno
This will generate the following files:
5. Please email to tathornt@uw.edu for any further questions. Enjoy!