computePvalues: Calculate P-values

Description Usage Arguments Value See Also Examples

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

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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

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ods <- makeExampleOutriderDataSet()

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

ods <- computePvalues(ods)

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

gagneurlab/OUTRIDER documentation built on Oct. 24, 2020, 6:49 p.m.