egscore.old: Fast score test for association, corrected with PC

In GenABEL: genome-wide SNP association analysis

Description

Fast score test for association between a trait and genetic polymorphism, adjusted for possible stratification by principal components.

Usage

egscore.old(formula,data,snpsubset,idsubset,kinship.matrix,naxes=3,strata,
				times=1,quiet=FALSE,bcast=10,clambda=TRUE,propPs=1.0) 

Arguments

formula	Formula describing fixed effects to be used in analysis, e.g. y ~ a + b means that outcome (y) depends on two covariates, a and b. If no covariates used in analysis, skip the right-hand side of the equation.
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/cc are used for analysis.
kinship.matrix	kinship matrix, as returned by ibs, (use weight="freq"!)
naxes	Number of axes of variation to be used in adjustment (should be much smaller than number of subjects)
strata	Stratification variable. If provieded, scores are computed within strata and then added up.
times	If more then one, the number of replicas to be used in derivation of empirical genome-wide significance.
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

Details

The idea of this test is to use genomic kinship matrix to first, derive axes of genetic variation (principal components), and, second, adjust both trait and genotypes onto these axes.

The traits is first analysed using LM and with covariates as specified with formula and also with axes of variation as predictors. Corrected genotypes are defined as residuals from regression of genotypes onto axes (which are orthogonal). Correlaton between corrected genotypes and phenotype is computed, and test statistics is defined as square of this correlation times (N - K - 1), where N is number of genotyped subjects and K is the number of axes.

This test is defined only for 1 d.f.

Value

Object of class scan.gwaa-class

Author(s)

Yurii Aulchenko

References

Price A. L. et al, Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.

See Also

qtscore, mmscore, ibs, scan.gwaa-class

Examples

#data(ge03d2ex)
##egscore.old with stratification
#gkin <- ibs(ge03d2ex,w="freq")
#a <- egscore.old(dm2~sex+age,data=ge03d2ex,kin=gkin)
#plot(a,df="Pc1df")

Example output

Loading required package: MASS
Loading required package: GenABEL.data

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