Figure 1
From: An efficient algorithm to perform multiple testing in epistasis screening
Input/output formats of MBMDR-3.0.3. MBMDR-3.0.3 takes as argument a text file (possibly converted by our software from PLINK format) containing the trait and SNP values of the subjects under study and a set of command line parameters. If the ath subject is a case (control), c a =1(0) (a=1…s). S N P b is a label referring to the bth SNP (b=1,…M). The genotype of an individual a at locus b is denoted as g a b (0 if homozygous for the first allele, 1 if heterozygous and 2 if homozygous for the second allele). The produced output is a text file containing the most significant SNP pairs in relation with the trait. (S N P l j ,S N P r j ) refers to the jth best SNP pair, i.e. the pair with the jth lowest p-value p j . Our software has only one mandatory argument: the scale of the trait. Use either −−binary for a binary trait, or −−continuous for a continuous scale, or −−survival for a censored trait (in this case the trait column is replaced by two columns, one for the time variable and one for the censoring variable). We have developed an interactive help, accessible through −−help, describing all other options. For instance, -n sets the amount of p-values to compute (default: 1000), -p sets the amount of permutations to asses statistical significance (default: 999).