GenABEL (version 1.8-0)

estlambda: Estimate the inflation factor for a distribution of P-values

Description

Estimate the inflation factor for a distribution of P-values or 1df chi-square test. The major use of this procedure is the Genomic Control, but can also be used to visualise the distribution of P-values coming from other tests. Methods implemented include 'median' (median(chi2)/0.455...), regression (of observed onto expected) and 'KS' (optimizing the chi2.1df distribution fit by use of Kolmogorov-Smirnov test)

Usage

estlambda(data, plot = FALSE, proportion = 1, method = "regression", filter = TRUE, df = 1, ...)

Arguments

data

A vector of reals. If all are

plot

Whether the plot should be shown or not (default).

proportion

The proportion of lowest P (or $chi^2$) values to be used when estimating the inflation factor $lambda$.

method

"regression" (default), "median", or "KS": method to be used for $lambda$ estimation.

filter

if the test statistics with 0-value of $chi^2$ should be excluded prior to estimation of $lambda$.

df

Number of degrees of freedom.

...

arguments passed to the plot function.

Value

A list with elements

estimate

Estimate of $lambda$

se

Standard error of the estimate

See Also

ccfast, qtscore

Examples

require(GenABEL.data)
data(srdta)
pex <- summary(gtdata(srdta))[,"Pexact"]
estlambda(pex, plot=TRUE)
estlambda(pex, method="regression", proportion = 0.95)
estlambda(pex, method="median")
estlambda(pex, method="KS")
a <- qtscore(bt,srdta)
lambda(a)