computePvalues: Calculate P-values

In OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

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]

OUTRIDER documentation built on Nov. 8, 2020, 5:16 p.m.