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estlambda {GenABEL}

Estimate the inflation factor for a distribution of P-values
Package: 
GenABEL
Version: 
1.8-0

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 <=1, it is assumed that this is a vector of P-values, else it is treated as a vector of chi-squares
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.

Values

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)

Author(s)

Yurii Aulchenko

Documentation reproduced from package GenABEL, version 1.8-0. License: GPL (>= 2)