R: Transmission/disequilibrium test of a multiallelic marker

mtdt {gap} | R Documentation

## Transmission/disequilibrium test of a multiallelic marker

### Description

This function calculates transmission-disequilibrium statistics involving multiallelic marker.

Inside the function are tril and triu used to obtain lower and upper triangular matrices.

### Usage

    mtdt(x,n.sim=0)

### Arguments

`x` | the data table
`n.sim` | the number of simulations

### Value

It returned list contains the following components:

`SE` | Spielman-Ewens Chi-square from the observed data
`ST` | Stuart or score Statistic from the observed data
`pSE` | the simulated p value
`sSE` | standard error of the simulated p value
`pST` | the simulated p value
`sST` | standard error of the simulated p value

### References

Miller MB (1997) Genomic scanning and the transmission/disequilibrium test: analysis of error rates. Genet. Epidemiol. 14:851-856

Sham PC (1997) Transmission/disequilibrium tests for multiallelic loci. Am. J. Hum. Genet. 61:774-778

Spielman RS, Ewens WJ (1996) The TDT and other family-based tests for linkage disequilibrium and association. Am. J. Hum. Genet. 59:983-989

Zhao JH, Sham PC, Curtis D (1999) A program for the Monte Carlo evaluation of significance of the extended transmission/disequilibrium test. Am. J. Hum. Genet. 64:1484-1485

### Author(s)

Mike Miller, Jing Hua Zhao

### See Also

`bt`

### Examples

    ## Not run:
    # Copeman et al (1995) Nat Genet 9: 80-5

    x <- matrix(c(0,0, 0, 2, 0,0, 0, 0, 0, 0, 0, 0,
                  0,0, 1, 3, 0,0, 0, 2, 3, 0, 0, 0,
                  2,3,26,35, 7,0, 2,10,11, 3, 4, 1,
                  2,3,22,26, 6,2, 4, 4,10, 2, 2, 0,
                  0,1, 7,10, 2,0, 0, 2, 2, 1, 1, 0,
                  0,0, 1, 4, 0,1, 0, 1, 0, 0, 0, 0,
                  0,2, 5, 4, 1,1, 0, 0, 0, 2, 0, 0,
                  0,0, 2, 6, 1,0, 2, 0, 2, 0, 0, 0,
                  0,3, 6,19, 6,0, 0, 2, 5, 3, 0, 0,
                  0,0, 3, 1, 1,0, 0, 0, 1, 0, 0, 0,
                  0,0, 0, 2, 0,0, 0, 0, 0, 0, 0, 0,
                  0,0, 1, 0, 0,0, 0, 0, 0, 0, 0, 0),nrow=12)

    # See note to bt for the score test obtained by SAS

    mtdt(x)

    ## End(Not run)

[Package gap version 1.2.2 Index]