R: fast case-control analysis

ccfast {GenABEL} | R Documentation

## fast case-control analysis

### Description

Fast case-control analysis by computing chi-square test from 2x2 (allelic) or 2x3 (genotypic) tables

### Usage

    ccfast(y, data, snpsubset, idsubset, times=1, quiet=FALSE,bcast=10,
    		clambda=TRUE,propPs=1.0)

### Arguments

`y` | character name of the vector of case-control status. Cases are denoted as 1 and controls as 0.
`data` | An object of `gwaa.data-class`
`snpsubset` | Index, character or logical vector with subset of SNPs to run analysis on. If missing, all SNPs from `data` are used for analysis.
`idsubset` | Index, character or logical vector with subset of IDs to run analysis on. If missing, all people from `data` are used for analysis.
`times` | If more then one, the number of replicas to be used in derivation of empirical genome-wide significance. See `emp.qtscore`, which calls qtscore with times>1 for details
`quiet` | do not print warning messages
`bcast` | If the argument times > 1, progress is reported once in bcast replicas
`clambda` | If inflation facot Lambda is estimated as lower then one, this parameter controls if the original P1df (clambda=TRUE) to be reported in Pc1df, or the original 1df statistics is to be multiplied onto this "deflation" factor (clambda=FALSE). If a numeric value is provided, it is used as a correction factor.
`propPs` | proportion of non-corrected P-values used to estimate the inflation factor Lambda, passed directly to the `estlambda`

### Value

Object of class `scan.gwaa-class`

### Author(s)

Yurii Aulchenko

### See Also

`emp.ccfast`, `plot.scan.gwaa`, `scan.gwaa-class`

### Examples

    require(GenABEL.data)
    data(srdta)
    a <- ccfast("bt",data=srdta,snps=c(1:10),ids=c(1:100))
    a
    a <- ccfast("bt",data=srdta)
    plot(a)

[Package GenABEL version 1.8-0 Index]