# estlambda: Estimate the inflation factor for a distribution of P-values In GenABEL: genome-wide SNP association analysis

## 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

 ```1 2``` ``` 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

`ccfast`, `qtscore`

## Examples

 ```1 2 3 4 5 6 7 8 9``` ```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) ```

### Example output

```Loading required package: MASS
\$estimate
[1] 1.221399

\$se
[1] 0.02964587

\$estimate
[1] 1.221399

\$se
[1] 0.02964587

\$estimate
[1] 0.9069703

\$se
[1] NA

\$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
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
\$estimate
[1] 1

\$se
[1] NA
```

GenABEL documentation built on May 30, 2017, 3:36 a.m.