mffinder - A program to detect genetic interaction patterns in genetic data sets
mffinder [-dCvntxmSosl] input-file ACLength [minData ORPredis ORProt]
The minimum amount of information to be given to the program is an input file (see section 'The input file format') and the number of alleles which shall contistute the allele combinations (ACs; given by ACLength). Optionally minData specifies the minimum number of observations for an AC such that it is included in the output. ORPredis and ORProt are odds ratios which also constrain the output. If the OR as computed for an AC is smaller than ORPredis and bigger than ORProt this AC is not output. Options are as follows:
mffinder reads an input file given as a tab-separted ascii file. It contains both genotype and phenotype information on all individuals to be analyzed. The first line contains names of the columns. Each column holds genotype information for one locus except for the last column which holds the phenotype.
The locus names are ``locus1'', ``locus2'' and ``HLA'', respectively. The last column describes the phenotype irrespective of its name. All other lines occur in pairs with each pair describing an individual. Each line holds one allele observed at each locus in the same order as listed in the first line. The last number has to be the phenotype of the individual. The second line gives the second alleles of the genotypes of the individual and the phenotype is repeated in the last column. Missing data is represented as '.' (dot). All genotypes must be one or tow digit numbers and the phenotype must be either '0' or '1'.
The output starts with a line listing all loci for which the following analysis is conducted (quotes are inset):
Loci under scrutiny: IFNA1 TNFRSF1A-2 NFKBIA-6
Next for each penetrance model identical sections are being output.
Model: Additive Count of tests: 20609 Allele Combination CTU CAU CTA CAA FU FA RR p REE IFNA1:07, TNFRSF1A-2:02 1 1360 40 1580 0.0007 0.0253 34.43 0.0000 2.7846 IFNA1:07, NFKBIA-6:01 3 1324 44 648 0.0023 0.0679 29.97 0.0000 2.4073
The examples shows a excerpt from a concrete analysis. Here the Additive model is shown. The line Count of tests holds the information of how many test statistics were computed which can be used for some correction procedure. The next line describes the columns of the table listed from the 4th line on.
All following lines list ACs which satisfy the constraints given by certain arguments (minData, ORPredis ORProt). The next penetrance model is introduced by a Model: line.