computePvalues {OUTRIDER} | R Documentation

## Calculate P-values

### Description

This function computes the P-values based on the fitted negative binomial model. It computes two matrices with the same dimension as the count matrix (samples x genes), which contain the corresponding P-values and adjusted P-values of every count.

### Usage

    computePvalues(object, ...)

    ## S4 method for signature 'OutriderDataSet'
    computePvalues(
      object,
      alternative = c("two.sided", "greater", "less"),
      method = "BY",
      BPPARAM = bpparam()
    )

### Arguments

`object` | An OutriderDataSet
`...` | additional params, currently not used.
`alternative` | Can be one of "two.sided", "greater" or "less" to specify the alternative hypothesis used to calculate the P-values, defaults to "two.sided"
`method` | Method used for multiple testing
`BPPARAM` | Can be used to parallelize the computation, defaults to bpparam()

### Value

An OutriderDataSet object with computed nominal and adjusted P-values

### See Also

p.adjust

### Examples

    ods <- makeExampleOutriderDataSet()

    ods <- estimateSizeFactors(ods)
    ods <- fit(ods)

    ods <- computePvalues(ods)

    assays(ods)[['pValue']][1:10,1:10]

[Package OUTRIDER version 1.8.0 Index]