deseqInterest {IntEREst} | R Documentation

## DESeq2 analysis for IntEREst object

### Description

Differential intron retention test adapted from the `DESeq2` package.

### Usage

    deseqInterest (x, design, pAdjustMethod = "BH",
    	sizeFactor=c(), contrast, bpparam, ...)

### Arguments

`x` | Object of type `SummarizedExperiment`.
`design` | Formula specifying the design of the experiment. It must specify an interaction term between variables from column names of `sampleData(x)`.
`pAdjustMethod` | What adjustment method to be sed on the p-values. See p.adjust for more information.
`sizeFactor` | Numeric vector with the same size as the clolumn size of the count matrix in `x`, if defined it will be used for scaling of the count matrix.
`contrast` | Argument speciftying the comparison to extract from `x`. See `results` function in the `DESeq2` package for more information.
`bpparam` | An optional `BiocParallelParam` instance defining the parallel back-end to be used. If not defined the function will run sequentially (on a single computing core).
`...` | Other parameter settings for the results function in the `DESeq2` package.

### Value

a `DESeqResults` object.

### Author(s)

Ali Oghabian

### See Also

`exactTestInterest` `qlfInterest`, `treatInterest` `DEXSeqIntEREst`

### Examples

    mdsChr22IntObj<- mdsChr22Obj[rowData(mdsChr22Obj)$int_ex=="intron",]
    deseqRes<- deseqInterest(x=mdsChr22IntObj,
    	design=~test_ctrl, contrast=list("test_ctrl_test_vs_ctrl"))

    # Number of U12/U2 type significantly differential retained introns in chr22
    table(rowData(mdsChr22Obj)[which(deseqRes$padj<.01), "intron_type"])

[Package IntEREst version 1.18.0 Index]