variance_prior {glmGamPoi} | R Documentation

## Estimate the scale and df for a Inverse Chisquare distribution that generate the true gene variances

### Description

This function implements Smyth's 2004 variance shrinkage. It also supports covariates that are fitted to log(s2) with natural splines. This is based on the 2012 Lund et al. quasi-likelihood paper.

### Usage

    variance_prior(s2, df, covariate = NULL, abundance_trend = NULL)

### Arguments

`s2` | vector of observed variances. Must not contain `0`'s.
`df` | vector or single number with the degrees of freedom
`covariate` | a vector with the same length as s2. `covariate` is used to regress out the trend in `s2`. If `covariate = NULL`, it is ignored.
`abundance_trend` | logical that decides if the additional abundance trend is fit to the data. If `NULL` the abundance trend is fitted if there are more than 10 observations and the `covariate` is not `NULL`. Default: `NULL`

### Value

a list with three elements:

variance0

  estimate of the scale of the inverse Chisquared distribution. If covariate is `NULL` a single number, otherwise a vector of `length(covariate)`

df0

  estimate of the degrees of freedom of the inverse Chisquared distribution

var_pos

  the shrunken variance estimates: a combination of `s2` and `variance0`

### See Also

`limma::squeezeVar()`

[Package glmGamPoi version 1.6.0 Index]