c2bat {pbatR}

C2BAT

Description

C2BAT (c) Matt McQueen, Jessica Su, Christoph Lange.

Usage

c2bat(
  snps,
  case.aa, case.Aa, case.AA,
  control.aa, control.Aa, control.AA,
  replicates=0,
  statistic="armitage",
  method="exact")

Arguments

snps

Names of the snps (vector). Can be strings.

case.aa

Number of cases with aa genotype (a vector corresponding to the snps).

case.Aa

Number of cases with Aa genotype.

case.AA

Number of cases with AA genotype.

control.aa

Number of controls with aa genotype.

control.Aa

Number of controls with Aa genotype.

control.AA

Number of controls with AA genotype.

replicates

This value should be set to zero for the first analysis. Then, once the top snps have been selected, this should be rerun with replicates>1000 for those selected snps.

statistic

"armitage" = the Armitage trend test. "logrank" = logrank test

method

"exact" = exact likelihood function "approximate" = approximate likelihood function

Details

The output is formatted as follows: SNP, case.aa, case.Aa, case.AA, control.aa, control.Aa, control.AA, Monte-Carlo p-value, p-value, non-centrality parameter (for power calculations), modelc2-based OR, allelic OR.

Note that the non-centrality parameter and the ORs are independent of the pvalues.

Examples

## Not run: 
c2bat( snps=c("snp1","snp2"),
       case.aa=c(10,11), case.Aa=c(30,31), case.AA=c(14,44),
       control.aa=c(33,32), control.Aa=c(100,99), control.AA=c(0,0) )

## End(Not run)