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Last data update: 2014.03.03

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

estlambda

R Documentation

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 <=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.

Value

A list with elements

`estimate`	Estimate of lambda
`se`	Standard error of the estimate

Author(s)

Yurii Aulchenko

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(GenABEL)
Loading required package: MASS
Loading required package: GenABEL.data
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GenABEL/estlambda.Rd_%03d_medium.png", width=480, height=480)
> ### Name: estlambda
> ### Title: Estimate the inflation factor for a distribution of P-values
> ### Aliases: estlambda
> ### Keywords: htest
> 
> ### ** Examples
> 
> require(GenABEL.data)
> data(srdta)
> pex <- summary(gtdata(srdta))[,"Pexact"]
> estlambda(pex, plot=TRUE)
$estimate
[1] 1.221399

$se
[1] 0.02964587

> estlambda(pex, method="regression", proportion = 0.95)
$estimate
[1] 1.221399

$se
[1] 0.02964587

> estlambda(pex, method="median")
$estimate
[1] 0.9069703

$se
[1] NA

> estlambda(pex, method="KS")
$estimate
[1] 0.5000458

$se
[1] NA

Warning message:
In estlambda(pex, method = "KS") :
  using method='KS' lambda too close to limits, use other method
> a <- qtscore(bt,srdta)
Warning messages:
1: In test.type(y, trait.type) : binomial trait is analysed as gaussian
2: In qtscore(bt, srdta) : 11 observations deleted due to missingness
3: In qtscore(bt, srdta) : Lambda estimated < 1, set to 1
> lambda(a)
$estimate
[1] 1

$se
[1] NA

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>