estimateGLMTagwiseDisp: Empirical Bayes Tagwise Dispersions for Negative Binomial...

In edgeR: Empirical Analysis of Digital Gene Expression Data in R

Description

Compute an empirical Bayes estimate of the negative binomial dispersion parameter for each tag, with expression levels specified by a log-linear model.

Usage

## S3 method for class 'DGEList'
estimateGLMTagwiseDisp(y, design=NULL, prior.df=10,
            trend=!is.null(y$trended.dispersion), span=NULL, ...)
## Default S3 method:
estimateGLMTagwiseDisp(y, design=NULL, offset=NULL, dispersion,
            prior.df=10, trend=TRUE, span=NULL, AveLogCPM=NULL,
            weights=NULL, ...)

Arguments

y	matrix of counts or a DGEList object.
design	numeric design matrix, as for glmFit.
trend	logical. Should the prior be the trended dispersion (TRUE) or the common dispersion (FALSE)?
offset	offset matrix for the log-linear model, as for glmFit. Defaults to the log-effective library sizes.
dispersion	common or trended dispersion estimates, used as an initial estimate for the tagwise estimates.
prior.df	prior degrees of freedom.
span	width of the smoothing window, in terms of proportion of the data set. Default value decreases with the number of tags.
AveLogCPM	numeric vector giving average log2 counts per million for each tag
weights	optional numeric matrix giving observation weights
...	other arguments are passed to dispCoxReidInterpolateTagwise.

Details

This function implements the empirical Bayes strategy proposed by McCarthy et al (2012) for estimating the tagwise negative binomial dispersions. The experimental conditions are specified by design matrix allowing for multiple explanatory factors. The empirical Bayes posterior is implemented as a conditional likelihood with tag-specific weights, and the conditional likelihood is computed using Cox-Reid approximate conditional likelihood (Cox and Reid, 1987).

The prior degrees of freedom determines the weight given to the global dispersion trend. The larger the prior degrees of freedom, the more the tagwise dispersions are squeezed towards the global trend.

Note that the terms ‘tag’ and ‘gene’ are synonymous here. The function is only named ‘Tagwise’ for historical reasons.

This function calls the lower-level function dispCoxReidInterpolateTagwise.

Value

estimateGLMTagwiseDisp.DGEList produces a DGEList object, which contains the tagwise dispersion parameter estimate for each tag for the negative binomial model that maximizes the Cox-Reid adjusted profile likelihood. The tagwise dispersions are simply added to the DGEList object provided as the argument to the function.

estimateGLMTagwiseDisp.default returns a vector of the tagwise dispersion estimates.

Author(s)

Gordon Smyth, Davis McCarthy

References

Cox, DR, and Reid, N (1987). Parameter orthogonality and approximate conditional inference. Journal of the Royal Statistical Society Series B 49, 1-39.

McCarthy, DJ, Chen, Y, Smyth, GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 40, 4288-4297. https://doi.org/10.1093/nar/gks042

See Also

estimateGLMCommonDisp for common dispersion or estimateGLMTrendedDisp for trended dispersion in the context of a generalized linear model.

estimateCommonDisp for common dispersion or estimateTagwiseDisp for tagwise dispersions in the context of a multiple group experiment (one-way layout).

Examples

y <- matrix(rnbinom(1000,mu=10,size=10),ncol=4)
d <- DGEList(counts=y,group=c(1,1,2,2),lib.size=c(1000:1003))
design <- model.matrix(~group, data=d$samples) # Define the design matrix for the full model
d <- estimateGLMTrendedDisp(d, design, min.n=10)
d <- estimateGLMTagwiseDisp(d, design)
summary(d$tagwise.dispersion)

Example output

Loading required package: limma
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
0.04842 0.06727 0.07985 0.09595 0.11026 0.27510 

edgeR documentation built on Jan. 16, 2021, 2:03 a.m.