##TrioMDR: detecting SNP interactions in trio families with model-based multifactor dimensionality reduction
Description :This page includes the codes of TrioMDR which are implemented and tested on R version 3.2.4 by Mr. Liu (Jie Liu, Email:jiel@email.swu.edu.cn) and free for academic usage. You can run it at your own disk. For other purposes, please contact the corresponding Author Dr. Wang (JunWang, Email: kingjun@swu.edu.cn). If you have any problem on using these codes,just contact Dr. Wang via Email.
Usage: source("path/TrioMDR.R") results <- TrioMDR(Trios.file, K=2, classm='PDT', adj.main='FALSE', nperm=5)
Parameters: Trios.file: The PLINK format ped file. Not that the ped file should only contain numbers. See test.ped as an example (loucs 2 and 7 are disease loci). classm: classification rule to define H/L, default geno-PDT statistic adj.main: logical value, adjust marginal effect or not, default FALSE. nperm: number of permutation time to estimate non-central parameters, default 5
Column Number Description of Trios.file: 1 Pedigree number (must be an integer) 2 Individual ID number (must be an integer) 3 ID of father (0 if this individual is a founder) 4 ID of mother (0 if this individual is a founder) 5 Sex (1=male, 2=female, 0=unknown) 6 Disease status (2=affected, 1=unaffected, 0=unknown) 7 The 1rst allele pair (must be pairs of integers) 8 ... ... n-1 The 1rst allele of the last pair n