Score test for association in related people

mmscore {GenABEL}R Documentation

Score test for association in related people

Description

Score test for association between a trait and genetic polymorphism, in samples of related individuals

Usage

mmscore(h2object,data,snpsubset,idsubset,strata,times=1,quiet=FALSE,bcast=10,clambda=TRUE,propPs=1.0)

Arguments

h2object An object returned by polygenic polygenic mixed model analysis routine. The sub-objects used are measuredIDs, residualY, and InvSigma. One can supply mmscore with a fake h2object, containing these list elements.
data An object of gwaa.data-class. ALWAYS PASS THE SAME OBJECT WHICH WAS USED FOR ipolygenic ANALYSIS, NO SUB-SETTING IN IDs (USE IDSUBSET ARGUMENT FOR SUB-SETTING)!!!
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.
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. NOTE: The structure of the data is not exchangable, therefore do not use times > 1 unless you are really sure you understand what you are doing!
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

Score test is performed using the formula

\frac{((G-E[G]) V^{-1} residualY)^2}{(G-E[G]) V^{-1} (G-E[G])}

where G is the vector of genotypes (coded 0, 1, 2) and E[G] is a vector of (strata-specific) mean genotypic values; V^{-1} is the InvSigma and residualY are residuals from the trait analysis with polygenic procedure.

This test is similar to that implemented by Abecasis et al. (see reference).

Value

Object of class scan.gwaa-class; only 1 d.f. test is implemented currently.

Author(s)

Yurii Aulchenko

References

Chen WM, Abecasis GR. Family-based association tests for genome-wide association scans. Am J Hum Genet. 2007 Nov;81(5):913-26.

See Also

grammar, qtscore, egscore, plot.scan.gwaa, scan.gwaa-class

Examples

# ge03d2 is rather bad data set to demonstrate grammar, 
# because this is a population-based study
data(ge03d2.clean)
#take half for speed
ge03d2.clean <- ge03d2.clean[1:100,]
gkin <- ibs(ge03d2.clean,w="freq")
h2ht <- polygenic(height ~ sex + age,kin=gkin,ge03d2.clean)
h2ht$est
mm <- mmscore(h2ht,data=ge03d2.clean)
# compute grammar
gr <- qtscore(h2ht$pgres,data=ge03d2.clean,clam=FALSE)
#compute GC
gc <- qtscore(height ~ sex + age,data=ge03d2.clean)
#compare
plot(mm,df="Pc1df",cex=0.5)
add.plot(gc,df="Pc1df",col="red")
add.plot(gr,df="Pc1df",col="lightgreen",cex=1.1)
# can see that mmscore and grammar are quite the same... in contrast to GC

[Package GenABEL version 1.6-7 Index]