help clump

Title

Genetic association for chromosome data using a permutation test

Syntax

clump
[varlist]
[, options]

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.

Description

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

Examples

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

Author

Adrian Mander, MRC Biostatistics Unit, Cambridge, UK.

Email adrian.mander@mrc-bsu.cam.ac.uk

Also see

Related commands

HELP FILES SSC installation links Description

gipf (if installed) (ssc install gipf) Graphical representation of a log-linear model

hapipf (if installed) (ssc install hapipf) Haplotype frequency estimation using log-linear models