predFC {edgeR} | R Documentation

## Predictive log-fold changes

### Description

Computes estimated coefficients for a NB glm in such a way that the log-fold-changes are shrunk towards zero.

### Usage

    ## S3 method for class 'DGEList'
    predFC(y, design, prior.count=0.125, offset=NULL, dispersion=NULL,
           weights=NULL, ...)
    ## S3 method for class 'SummarizedExperiment'
    predFC(y, design, prior.count=0.125, offset=NULL, dispersion=NULL,
           weights=NULL, ...)
    ## Default S3 method:
    predFC(y, design, prior.count=0.125, offset=NULL, dispersion=0,
           weights=NULL, ...)

### Arguments

`y` | a matrix of counts, or a `DGEList` object, or a `SummarizedExperiment` object
`design` | the design matrix for the experiment
`prior.count` | the average prior count to be added to each observation. Larger values produce more shrinkage.
`offset` | numeric vector or matrix giving the offset in the log-linear model predictor, as for `glmFit`. Usually equal to log library sizes.
`dispersion` | numeric vector of negative binomial dispersions.
`weights` | optional numeric matrix giving observation weights
`...` | other arguments are passed to `glmFit`.

### Details

This function computes predictive log-fold changes (pfc) for a NB GLM. The pfc are posterior Bayesian estimators of the true log-fold-changes. They are predictive of values that might be replicated in a future experiment.

Specifically, the function adds a small prior count to each observation before fitting the GLM (see `addPriorCount` for details). The actual prior count that is added is proportion to the library size. This has the effect that any log-fold-change that was zero prior to augmentation remains zero and non-zero log-fold-changes are shrunk towards zero.

The prior counts can be viewed as equivalent to a prior belief that the log-fold changes are small, and the output can be viewed as posterior log-fold-changes from this Bayesian viewpoint. The output coefficients are called predictive log fold-changes because, depending on the prior, they may be a better prediction of the true log fold-changes than the raw estimates.

Log-fold changes for genes with low counts are shrunk more than those for genes with high counts. In particular, infinite log-fold-changes arising from zero counts are avoided. The exact degree to which this is done depends on the negative binomail dispersion.

### Value

Numeric matrix of (shrunk) linear model coefficients on the log2 scale.

### Author(s)

Belinda Phipson and Gordon Smyth

### References

Phipson, B. (2013). Empirical Bayes modelling of expression profiles and their associations. PhD Thesis. University of Melbourne, Australia. http://repository.unimelb.edu.au/10187/17614

### See Also

`glmFit`, `exactTest`, `addPriorCount`

### Examples

    # generate counts for a two group experiment with n=2 in each group and 100 genes
    disp <- 0.1
    y <- matrix(rnbinom(400,size=1/disp,mu=4), nrow=100, ncol=4)
    y <- DGEList(y, group=c(1,1,2,2))
    design <- model.matrix(~group, data=y$samples)

    #estimate the predictive log fold changes
    predlfc <- predFC(y, design, dispersion=disp, prior.count=1)
    logfc <- predFC(y,design,dispersion=disp, prior.count=0)
    logfc.truncated <- pmax(pmin(logfc,100),-100)

    #plot predFC's vs logFC's
    plot(predlfc[,2], logfc.truncated[,2],
         xlab="Predictive log fold changes", ylab="Raw log fold changes")
    abline(a=0,b=1)

[Package edgeR version 3.34.1 Index]