overdispersion_shrinkage {glmGamPoi} | R Documentation

## Shrink the overdispersion estimates

### Description

Low-level function to shrink a set of overdispersion estimates following the quasi-likelihood and Empirical Bayesian framework.

### Usage

    overdispersion_shrinkage(
      disp_est,
      gene_means,
      df,
      disp_trend = TRUE,
      ql_disp_trend = NULL,
      ...,
      verbose = FALSE
    )

### Arguments

`disp_est` | vector of overdispersion estimates
`gene_means` | vector of average gene expression values. Used to fit `disp_trend` if that is `NULL`.
`df` | degrees of freedom for estimating the Empirical Bayesian variance prior. Can be length 1 or same length as `disp_est` and `gene_means`.
`disp_trend` | vector with the dispersion trend. If `NULL` or `TRUE` the dispersion trend is fitted using a (weighted) local median fit. Default: `TRUE`.
`ql_disp_trend` | a logical to indicate if a second abundance trend using splines is fitted for the quasi-likelihood dispersions. Default: `NULL` which means that the extra fit is only done if enough observations are present.
`...` | additional parameters for the `loc_median_fit()` function
`verbose` | a boolean that indicates if information about the individual steps are printed while fitting the GLM. Default: `FALSE`.

### Details

The function goes through the following steps

1. Fit trend between overdispersion MLE's and the average gene expression. Per default it uses the `loc_median_fit()` function.

2. Convert the overdispersion MLE's to quasi-likelihood dispersion estimates by fixing the trended dispersion as the "true" dispersion value: disp_ql = (1 + mu * disp_mle) / (1 + mu * disp_trend)

3. Shrink the quasi-likelihood dispersion estimates using Empirical Bayesian variance shrinkage (see Smyth 2004).

### Value

the function returns a list with the following elements

dispersion_trend

  the dispersion trend provided by `disp_trend` or the local median fit.

ql_disp_estimate

  the quasi-likelihood dispersion estimates based on the dispersion trend, `disp_est`, and `gene_means`

ql_disp_trend

  the `ql_disp_estimate` still might show a trend with respect to `gene_means`. If `ql_disp_trend = TRUE` a spline is used to remove this secondary trend. If `ql_disp_trend = TRUE` it corresponds directly to the dispersion prior

ql_disp_shrunken

  the shrunken quasi-likelihood dispersion estimates. They are shrunken towards `ql_disp_trend`.

ql_df0

  the degrees of freedom of the empirical Bayesian shrinkage. They correspond to spread of the `ql_disp_estimate`'s

### References

- Lund, S. P., Nettleton, D., McCarthy, D. J., & Smyth, G. K. (2012). Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Statistical Applications in Genetics and Molecular Biology, 11(5). https://doi.org/10.1515/1544-6115.1826.

- Smyth, G. K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, 3(1). https://doi.org/10.2202/1544-6115.1027

### See Also

`limma::squeezeVar()`

### Examples

     Y <- matrix(rnbinom(n = 300 * 4, mu = 6, size = 1/4.2), nrow = 30, ncol = 4)
     disps <- sapply(seq_len(nrow(Y)), function(idx){
       overdispersion_mle(Y[idx, ])$estimate
     })
     shrink_list <- overdispersion_shrinkage(disps, rowMeans(Y), df = ncol(Y) - 1,
                                             disp_trend = FALSE, ql_disp_trend = FALSE)

     plot(rowMeans(Y), shrink_list$ql_disp_estimate)
     lines(sort(rowMeans(Y)), shrink_list$ql_disp_trend[order(rowMeans(Y))], col = "red")
     points(rowMeans(Y), shrink_list$ql_disp_shrunken, col = "blue", pch = 16, cex = 0.5)

[Package glmGamPoi version 1.4.0 Index]