fitDTU {satuRn} | R Documentation

## fitDTU

### Description

Parameter estimation of quasi-binomial models.

### Usage

    fitDTU(object, ...)

    ## S4 method for signature '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. 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 in the experiment. 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(s)

Jeroen Gilis

### Examples

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

[Package satuRn version 1.0.0 Index]