estimateDispersions {DEXSeq} | R Documentation |
This function obtains dispersion estimates for negative binomial distributed data for the specific case for DEXSeq.
## S4 method for signature 'DEXSeqDataSet' estimateDispersions( object, fitType=c("parametric","local","mean"), maxit=100, niter=10, quiet=FALSE, formula=design(object), BPPARAM=SerialParam())
object |
A DEXSeqDataSet |
fitType |
Either "parametric", "local", or "mean" for the type of fitting of dispersions to the mean intensity. See ?estimateDispersions,DESeqDataSet-method for details. |
maxit |
Control parameter: maximum number of iterations to allow for convergence |
niter |
Number of times to iterate between estimation of means and estimation of dispersion. |
quiet |
Whether to print messages at each step |
formula |
Formula used to fit the dispersion estimates |
BPPARAM |
A "BiocParallelParam" instance.
See |
See ?estimateDispersions,DESeqDataSet-method for details.
A DEXSeqDataSet with the dispersion information filled in as metadata columns.
data(pasillaDEXSeqDataSet, package="pasilla") dxd <- estimateSizeFactors( dxd ) dxd <- estimateDispersions( dxd )