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 1.2.0 Index]