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| statistical analysis of haplotype-disease association | ||
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HAPSTAT supports data from cross-sectional, longitudinal, case-control, and cohort (including case-cohort and nested case-control) association studies. The cross-sectional and longitudinal designs collect data on a random sample of individuals. In a cross-sectional study, the response variable is measured only once on all study subjects; in a longitudinal study, the response variable is measured repeatedly through time. In the case-control design, data is collected on a sample of diseased individuals or cases and a sample of disease-free individuals or controls. The cohort design follows a sample of at-risk individuals over time and records their times of disease occurrence. The individuals who are withdrawn prematurely or who are disease-free at the end of the cohort study have censored observations, in that their ages at onset are only known to be beyond their durations of follow-up. HAPSTAT also supports the inclusion of external genotype data collected on family trios or unrelated individuals, allowing for analysis on untyped SNPs.
HAPSTAT accepts ANSI-encoded text files containing data in a tabular (row-column) format. Each row contains space or tab delimited data specific to an individual. Column titles may be specified in the first line of the file and must also be space or tab delimited. If using external data, column titles must be specified in both the study file and the external file. File may contain columns of extraneous data. There are no requirements on the ordering of the columns.
The study file must contain one or more columns representing the multi-SNP genotype. Optionally, the file may include one or more columns of environmental covariates. Study-dependent data requirements are as follows:
The external file contains data collected on either trios or unrelated individuals. The file must contain one or more columns representing each of the SNP sites intended for analysis in the study file and all untyped SNPs of interest. For trio data, HAPSTAT requires three rows of data per family, where data for mothers and fathers is in the first two rows and the child's data is in the third. The correspondence between SNP sites in the study data and external data is determined by the column title. For both the study file and the external file, column titles must be specified in the first row of the file and the corresponding SNP sites must be titled the same in both files.
The multi-SNP genotype is represented by a sequence of the values 0, 1 and 2, corresponding to the number of occurrences of a specific allele at each SNP site. Any value other than 0, 1 or 2 is assumed to indicate missing SNP data. Individuals are allowed to have missing data at all SNP sites. Environmental covariates are represented by decimal values and may not contain missing values. The representation of data not intended for analysis is unimportant.
In cross-sectional studies, disease-related traits are represented by decimal values. In longitudinal studies, the identifier is represented as a string value and disease-related traits are represented by decimal values. HAPSTAT allows both quantitative and binary traits in cross-sectional studies and only quantitative traits in longitudinal studies. In case-control studies, the disease status is specified by 1 for cases or 0 for controls. In cohort studies, decimal values represent the observation times and a binary event indicator distinguishes between uncensored and censored individuals by the values 1 and 0, respectively.
The file case-control.dat, shown below, contains simulated data for a case-control study of 2000 individuals genotyped at five SNPs, where some SNP values are missing.
The disease status is specified in the first column, titled “Status”. The columns “Age” and “Gender” contain environmental covariate data, and the columns SNP1-SNP5 represent the five SNP sites. The ‘·’ character indicates a missing SNP value.
For external data, the sequence of values representing the genotype must have the same allele correspondence as in the study data. The file trio.dat, shown below, contains simulated data for 50 families genotyped at five SNPs. Columns SNP1-SNP5 correspond to the five identically titled SNP sites in case-control.dat.
To open a study file in HAPSTAT, select the menu
option File»Open and
choose the study type corresponding to your data from the submenu. Browse
to the directory where your data file resides, select your file and click
the Open button. The HAPSTAT display
after importing case-control.dat is shown in
You may only have one file open in HAPSTAT at any time. To open a new file,
select the menu option
File»Open
or click the icon 
on the toolbar. HAPSTAT will prompt you to save your
results before closing the current file. You may also close a file via the
menu option File»Close
or the icon 
on the
toolbar.
Use the Settings»Transpose menu option to transpose rows and columns.
To specify the columns that correspond to the variables HAPSTAT should use for
analysis, first click inside the text area of the variable you wish to set in
the Variables box on the right panel. Then select the columns of data
corresponding to that variable by clicking on the column labels on the left
panel. Use the toolbar icons
and
to show or hide unselected columns. The selection of variables for the
single-gene analysis of
case-control.dat
is shown in
Click the 
icon on the
toolbar to create multiple genes.
HAPSTAT will attempt to detect if the first line of your file contains column titles or actual data. You can toggle what HAPSTAT decides by checking/unchecking the menu option Settings»Include header.
To change your variable selections after the Continue button is clicked, return to the file tab and click the Edit button. The Settings»Clear menu option will clear the current selection.
Right click on the title of the column you wish to sort by and select Sort ascending or Sort descending. All columns are sorted accordingly.
All rows are included by default. To exclude a particular row from your analysis, right click on the row number and select Exclude.
You may import external data at any time. To open an external file, select the
menu option File»Open»External data file
and choose the external type corresponding to your data from the submenu.
Browse to the directory where your data file resides, select your file and
click the Open button. The HAPSTAT display after importing
trio.dat is shown in
If a study file is already open in HAPSTAT, all gene variables selected from the study file will be pre-selected from the external file (if present). You may add or remove SNP variables from the gene selection as described above. SNPs selected from the study file must be a subset of those selected from the external file. SNPs selected from the external file that are not selected or not present in the study file are considered to be untyped.