emp.ccfast: Genome-wide significance for a case-control GWA scan

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Genome-wide significance for a case-control GWA scan. Analysis function is ccfast.

Usage

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emp.ccfast(y, data, snpsubset, idsubset, times = 200, quiet=FALSE,
		bcast = 10)

Arguments

All arguments are the same as in and passed intact to the ccfast. See help for this function.

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

Details

In the analysis of empirical significance, first time the function ccfast is called and result object is saved. Later, the function ccfast is called times times with replace=FALSE in order to generate the distribution under the null. Each call, minimal P-value is extracted and compared with original P-values. For a particular SNP, empirical P-value is obtained as a proportion of times minimal Ps from resampled data was less then the original P.

The list elements effB, effAB and effBB are the ones obtained from the analysis of the original (not permuted) data set

Value

Object of class scan.gwaa-class

Author(s)

Yurii Aulchenko

See Also

ccfast, emp.qtscore, scan.gwaa-class

Examples

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require(GenABEL.data)
data(srdta)
a<-ccfast("bt",data=srdta,snps=c(500:800))
plot(a)
# this does not make sense, as the whole experiment must be analysed, not a small region!
# also, times = 20 is way too small (should be at least 200)
b<-emp.ccfast("bt",data=srdta,snps=c(500:800),bcast=10, times = 20)
plot(b)
# compare qvalues and empirical P
qv<-qvaluebh95(a[,"P1df"])$qval
qv
b[,"P1df"]
plot(qv,b[,"P1df"],xlim=c(0,1),ylim=c(0,1))
abline(a=0,b=1)

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