Focused Interaction Testing Framework (FITF) Software
The FITF software is being freely distributed to all interested investigators. The FITF application requires Windows 95, 98, NT, 2000, ME or XP to run. There are no guarantees offered for this software; the user assumes all risk. It is designed for case-control studies involving diallelic candidate genes. A full description of the method can be found in the following article:
The application can be run from a DOS prompt or simply by double-clicking on the program icon in Windows Explorer. The following files are needed:
FITF.exe – This is the application.
Maxfun.dll – This is the .dll used for maximization of the likelihood. (It just needs to be included in same directory). We thank Dr. Robert Elston for permission to use the maximization program Maxfun.
nparm.txt – This file contains settings for the input parameters. The first line of text contains labels and is not used in the program. The second line includes parameter settings separated by spaces, corresponding in order to the parameters specified in the first line. These parameters are:
‘iter’ the number of data sets to be analyzed
‘ss’ sample size, the number of cases + controls
‘cssc2’ the CSS cutoff for second stage tests (the recommended value is 3)
‘css3’ the CSS cutoff for third stage tests (the recommended value is 6)
‘alpha1’ total alpha level allocated to first stage tests
‘alpha2’ total alpha level allocated to second stage tests
‘alpha3’ total alpha level allocated to third stage tests
For example, for an experiment-wise alpha level of 0.05, the investigator may decide to allocate a third, 0.016667, to each stage by setting alpha1, alpha2, and alpha3 to 0.016667.
‘ng’ number of diallelic candidate genes in the data set to be analyzed
‘co’ 0: compute the CSS statistic using both cases and controls or 1: compute the CSS statistic using cases only. The authors recommend keeping this parameter set to 0, because computing the CSS statistic on controls only (although more powerful) may result in an inflated type I error rate.
dat1.txt – This is the data set to be analyzed. If there are multiple data sets to be analyzed, they should be named dat1.txt, dat2.txt, …. The total number of data sets will correspond to the ‘iter’ parameter. The first line of text is for the users benefit and is not used by the program. Following the first line, the data structure is as follows:
All data are space delimited.
The first column is an ID variable but is not used by the program.
The second column denotes disease status and must be coded 0: not affected, and 1: affected.
The third and subsequent columns denote diallelic candidate genes (or other categorical variables with less then or equal to 3 levels) and must be coded 0, 1, and 2. (An example data set is provided)
To run the program:
1) Store the previous files in a single directory.
2) Double click on FITF.exe
A text file, named ‘results.txt’, will be produced in the same directory that contains the results from the analysis of the data set(s) (an example results file is provided). The structure of results.txt is as follows:
First row: labels
First column: ‘iter’, an index that corresponds to the data set that was analyzed.
Second column: ‘Stage’, specifies whether the result is from the first (marginal effects), second (first order interactions), or third (second order interactions) stage of the analysis.
Third and forth columns: ‘cssc2’ and ‘cssc3’, CSS cutoff values for the second and third stages of the analysis.
Fifth column: ‘FDR-cutoff’, cutoff value below which the p-value is considered statistically significant.
Sixth column: ‘p-value’, unadjusted p-value. Only results with an unadjusted p-value below 0.1 are included in the file.
Seventh, eighth, and ninth columns: number(s) between 1 and ng that identifies the genes that produced the test result. Genes are identified by column in the input file with the third column identified as ‘1’, the forth as ‘2’, etc.
Downloading the
program:
The program can be downloaded by clicking here and selecting save on the dialog that appears.
The zip file contains the instructions and all the files mentioned in this document.