emp.qtscore: Genome-wide significance for a GWA scan
In GenABEL: genome-wide SNP association analysis

Description Usage Arguments Details Value Author(s) See Also Examples

Genome-wide significance for a GWA scan. Analysis function is qtscore.

1 2	emp.qtscore(formula , data, snpsubset, idsubset, strata, trait.type="gaussian", times = 200, quiet=FALSE, bcast = 10)

All arguments are the same as in and passed intact to the qtscore. See help for this function.

`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". If not specified, the procedure quesses the type
`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

In the analysis of empirical significance, first time the function qtscore is called and result object is saved. Later, the function qtscore is called times times with replace=FALSE in order to generate distribution under the null. Each call, minimal P-value is extracted and compared with original P-values. For a particular SNP, empirical P-value is obtained as a proportion of times minimal Ps from resampled data was less then original P.

The list elements effB, effAB and effBB are the ones obtained from the analysis of the original (not permuted) data set

The function does not yet implement correct analysis for X-linked data.

Object of class scan.gwaa-class

Yurii Aulchenko

qtscore, emp.ccfast, scan.gwaa-class

require(GenABEL.data)
data(srdta)
a<-qtscore(qt3~age+sex,data=srdta,snps=c(1:200))
plot(a)
# this does not make sense, as the whole experiment must be analysed, not a small region!
# also, times = 20 is way too small (should be at least 200)
b<-emp.qtscore(qt3~age+sex,data=srdta,snps=c(1:200), times = 20)
plot(b)

Loading required package: MASS
Loading required package: GenABEL.data
Warning messages:
1: In qtscore(qt3 ~ age + sex, data = srdta, snps = c(1:200)) :
  11 observations deleted due to missingness
2: In qtscore(qt3 ~ age + sex, data = srdta, snps = c(1:200)) :
  Lambda estimated < 1, set to 1

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Warning messages:
1: In qtscore(formula = formula, data = data, snpsubset = snpsubset,  :
  11 observations deleted due to missingness
2: In qtscore(formula = formula, data = data, snpsubset = snpsubset,  :
  Lambda estimated < 1, set to 1