R: 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 i`polygenic` 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,
    # because this is a population-based study
    require(GenABEL.data)
    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 1.8-0 Index]