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Genetic association for chromosome data using a permutation test


clump [varlist] [, options]

options Description ------------------------------------------------------------------------- Main lrchi2 specifies whether to use the likelihood ratio test. noise specifies . maxiter specifies the maximum number of iterations. -------------------------------------------------------------------------

Note: the first variable is the case/control variable that has to be binary. The next pair of variables are the pairs of alleles at the marker in question. A line of data represents one subject.


This program assesses the significance of the departure of observed values in a contingency table from the expected values conditional on the marginal totals. The present implementation works on 2 x N tables and was designed for use in genetic case-control association studies, but the program should be useful for any 2 x N contingency table, especially where N is large and the table is sparse. The significance is assessed using a Monte Carlo approach, by performing repeated simulations to generate tables having the same marginal totals as the one under consideration, and counting the number of times that a chi-squared value associated with the real table is achieved by the randomly simulated data. This means that the significance levels assigned should be unbiased (with accuracy dependent on the number of simulations performed) and that no special account needs to be taken of continuity corrections or small expected values.

The method is described in full in: Sham PC & Curtis D. 1995. Monte Carlo tests for associations between disease and alleles at highly polymorphic loci. Ann Hum Genet. 59: 97-105.

Options +------+ ----+ Main +-------------------------------------------------------------

lrchi2 specifies use of the likelihood ratio test on the 2 by 2 table. If a table contains a 0 cell the test statistic is missing.

noise displays chi-squared tables on original data

maxiter(#) max iterations for the permutation test


. clump cc a1628 b1628, noi maxiter(200) lrchi2

Author Adrian Mander, MRC Biostatistics Unit, Cambridge, UK. Email

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