diffSpliceDGEWrapper {diffUTR} | R Documentation

## DEUwrappers

### Description

Wrappers around commonly-used DEU methods (`diffSpliceDGE`, `DEXSeq` and an improved version of `diffSplice`

### Usage

    diffSpliceDGEWrapper(
      se,
      design,
      coef = NULL,
      QLF = TRUE,
      robust = TRUE,
      countFilter = TRUE,
      excludeTypes = NULL
    )

    diffSpliceWrapper(
      se,
      design,
      coef = NULL,
      robust = TRUE,
      improved = TRUE,
      countFilter = TRUE,
      excludeTypes = NULL
    )

    DEXSeqWrapper(
      se,
      design = ~sample + exon + condition:exon,
      reducedModel = ~sample + exon,
      excludeTypes = NULL,
      ...
    )

### Arguments

`se` | A bin-wise SummarizedExperiment as produced by `countFeatures`
`design` | A formula (using columns of 'colData(se)') or (for 'diffSpliceWrapper' or 'diffSpliceDGEWrapper' only) a model.matrix.
`coef` | The coefficient to be tested (ignored for 'DEXSeqWrapper').
`QLF` | Logical; whether to use edgeR's quasi-likelihood negative binomial (applicable only to 'diffSpliceDGEWrapper').
`robust` | Logical; whether to use robust fitting for the dispersion trend (ignored for 'DEXSeqWrapper').
`countFilter` | Logical; whether to filter out low-count bins (ignored for 'DEXSeqWrapper').
`excludeTypes` | A vector of bin types to ignore for testing. To test for any kind of differential usage, leave empty. To test for differential UTR usage, use 'excludeTypes=c("CDS","non-coding")' (or see `geneLevelStats` for more options).
`improved` | Logical; whether to use `diffSplice2` instead of the original `diffSplice` (default TRUE).
`reducedModel` | A reduced formula (applicable only to 'DEXSeqWrapper').
`...` | Further arguments (passed to 'testForDEU' and 'estimateExonFoldChanges') of 'DEXSeq'. Can for instance be used to enable multithreading, by passing 'BPPARAM=BiocParallel::MulticoreParam(ncores)'.

### Value

The 'se' object with additional rowData columns contain bin (i.e. exon) -level statistics, and a metadata slot containing gene level p-values.

### Examples

    library(SummarizedExperiment)
    data(example_bin_se)
    se <- diffSpliceWrapper(example_bin_se, ~condition)
    head(rowData(se))

[Package diffUTR version 1.0.0 Index]