GetStabilityGLM {GeneSelector} | R Documentation

## Stability measures for significance findings

### Description

Assesses the stability of the set of genes declared statistically significant for differential expression. To this end, p-values or adjusted p-values are used to generate binary response variables for a logistic regression model. As single covariate, the ranks obtained from the original dataset are used. Analogously to the linear model approach, weights are incorporated to attribute more importance to higher ranked genes. The deviance(s) resulting from these models are used as stability measure.

### Usage

    GetStabilityGLM(RR, decay = c("linear", "quadratic", "exponential"),
                    scheme = c("rank", "pval"), alpha = 1,
                    maxpval = 0.05, method=c("raw", "BH", "qvalue", "Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BY"))

### Arguments

`RR` | An object of class RepeatRanking.
`scheme` | Whether ranks (`scheme="rank"`) or p-values (`scheme="pval"`) should be used as basis of weighting.
`decay` | argument controlling the weight decay for the weights used in the linear regression model. If `decay=linear`, then the weight of the s-th rank/p-value is `1/s`, if `decay=quadratic`, then the weight is `1/s^2` and if `decay=exponential`, then the weight is `exp(-s*alpha)`, where `alpha` is a tuning parameter specified via the argument `alpha`.
`alpha` | To be specified only if `decay="exponential"`, s. also GetAlpha.
`maxpval` | The maximum p-value that is still considered significant (type I error). Default is 0.05.
`method` | The method used for p-value adjustment, s. AdjustPvalues. If `method = "raw"`, then the raw p-values will be used.

### Value

An object of class `GetStabilityGLM`

### Author(s)

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

### See Also

GetRepeatRanking, GetStabilityLm, GetStabilityOverlap, GetStabilityPCA, RecoveryScore, GetAlpha

[Package GeneSelector version 1.2.0 Index]