GetAlpha {GeneSelector} | R Documentation

## Helper function for stability assessement.

### Description

Both GetStabilityLm and GetStabilityOverlap depend on a parameter `alpha` if `decay=exponential`. If the weights are based on ranks, then a nonlinear regression of the form
`pval = 1- exp(-alpha*rank)`
can be used to find an appropriate value for `alpha` via nonlinear least squares. In order to adjust for too 'optimistic' p-values, multiple testing adjustments should be used, s. AdjustPvalues.

### Usage

    GetAlpha(ranking, pval, alpha0 = 0.01)

### Arguments

`ranking` | A numeric vector of ranks, regarded as regressor.
`pval` | A numeric vector of p-values corresponding to the vector `ranking`.
`alpha0` | A starting value for the nonlinear least squares estimation procedure passed to nls

### Value

The nonlinear least squares estimator for `alpha`, s. description.

### Note

It is more or less equivalent to use a p-value based ranking instead of ranks combined with this procedure.

### Author(s)

Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix

### See Also

GetStabilityLm, GetStabilityOverlap, AdjustPvalues, nls

### Examples

    ### rankings
    ranks <- 1:100
    ### corresponding p-values
    pvals <- 1-exp(-0.01*ranks) + rnorm(100, sd=0.001)
    ### determine alpha
    alphaopt <- GetAlpha(ranks, pvals, alpha0 = 0.01)

[Package GeneSelector version 1.4.0 Index]