fitDTU

Parameter estimation of quasi-binomial models.

fitDTU(object, ...)

# S4 method for SummarizedExperiment
fitDTU(
  object,
  formula,
  parallel = FALSE,
  BPPARAM = BiocParallel::bpparam(),
  verbose = TRUE
)

Arguments

object

A `SummarizedExperiment` instance generated with the SummarizedExperiment function of the SummarizedExperiment package. Alternatively, a RangedSummarizedExperiment or a SingleCellExperiment object. In the assay slot, provide the transcript-level expression counts as an ordinary `matrix`, `DataFrame`, a `sparseMatrix` or a `DelayedMatrix`. The `rowData` slot must be a `DataFrame` object describing the rows, which must contain a column `isoform_id` with the row names of the expression matrix and a column `gene_id` with the corresponding gene identifiers of each transcript. `colData` is a `DataFrame` describing the samples or cells. Finally, specify the experimental design as a formula in the metadata slot. This formula must be based on the colData. See the documentation examples and the vignette for more details.

...

parameters including:

formula

Model formula. The model is built based on the covariates in the data object.

parallel

Logical, defaults to FALSE. Set to TRUE if you want to parallellize the fitting procedure.

BPPARAM

object of class bpparamClass that specifies the back-end to be used for computations. See bpparam in BiocParallel package for details.

verbose

Logical, should progress be printed?

Value

An updated `SummarizedExperiment` instance. The instance now includes a new list of models ("fitDTUModels") in its rowData slot, which can be accessed by rowData(object)[["fitDTUModels"]].

Author

Jeroen Gilis

Examples

data(sumExp_example, package = "satuRn")
sumExp <- fitDTU(
    object = sumExp_example,
    formula = ~ 0 + group,
    parallel = FALSE,
    BPPARAM = BiocParallel::bpparam(),
    verbose = TRUE
)