qtscore {GenABEL} | R Documentation |
Fast score test for association between a trait and genetic polymorphism
qtscore(formula,data,snpsubset,idsubset,strata,trait.type="gaussian",times=1,quiet=FALSE,bcast=10,clambda=TRUE,propPs=1.0,details=TRUE)
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. |
strata |
Stratification variable. If provieded, scores are computed within strata and then added up. |
trait.type |
"gaussian" or "binomial" |
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 |
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 |
when FALSE, only SNP and ID names are not reported in the returned object (saves some memory). This is experimental and will be not mantained anymore as soon as we achieve better memory efficiency for storage of SNP and ID names (currently default R character data type used) |
When formula contains covariates, the traits is analysed using GLM and later residuals used when score test is computed for each of the SNPs in analysis. For binary traits, residuals from GLM are transformed using exp(x)/(1+exp(x)).
With no adjustment for binary traits, 1 d.f., the test is equivalent to the Armitage test.
This is a valid function to analyse GWA data, including X chromosome. For X chromosome, stratified analysis is performed (strata=sex).
Object of class scan.gwaa-class
Yurii Aulchenko
mmscore
,
egscore
,
emp.qtscore
,
plot.scan.gwaa
,
scan.gwaa-class
data(srdta) #qtscore with stratification a <- qtscore(qt3~sex,data=srdta) plot(a) b <- qtscore(qt3,strata=srdta@phdata$sex,data=srdta) add.plot(b,col="green",cex=2) # qtscore with extra adjustment a <- qtscore(qt3~sex+age,data=srdta) a plot(a) # compare results of score and chi-square test for binary trait a1 <- ccfast("bt",data=srdta,snps=c(1:100)) a2 <- qtscore(bt,data=srdta,snps=c(1:100),trait.type="binomial") plot(a1,ylim=c(0,2)) add.plot(a2,col="red",cex=1.5) # the good thing about score test is that we can do adjustment... a2 <- qtscore(bt~age+sex,data=srdta,snps=c(1:100),trait.type="binomial") points(a2$map,-log10(a2$P1df),col="green")