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

estlambda {GenABEL} | 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

### 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)

[Package GenABEL version 1.8-0 Index]