ccfast: fast case-control analysis

In GenABEL: genome-wide SNP association 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)

GenABEL documentation built on May 30, 2017, 3:36 a.m.