mmscore {GenABEL} | R Documentation |
Score test for association between a trait and genetic polymorphism, in samples of related individuals
mmscore(h2object,data,snpsubset,idsubset,strata,times=1,quiet=FALSE,bcast=10,clambda=TRUE,propPs=1.0)
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 |
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).
Object of class scan.gwaa-class
; only 1 d.f. test is
implemented currently.
Yurii Aulchenko
Chen WM, Abecasis GR. Family-based association tests for genome-wide association scans. Am J Hum Genet. 2007 Nov;81(5):913-26.
grammar
,
qtscore
,
egscore
,
plot.scan.gwaa
,
scan.gwaa-class
# 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[1:450,] 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