computePvalues {OUTRIDER} | R Documentation |
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.
computePvalues(object, ...) ## S4 method for signature 'OutriderDataSet' computePvalues(object, alternative = c("two.sided", "greater", "less"), method = "BY", BPPARAM = bpparam())
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() |
An OutriderDataSet object with computed nominal and adjusted P-values
p.adjust
ods <- makeExampleOutriderDataSet() ods <- estimateSizeFactors(ods) ods <- fit(ods) ods <- computePvalues(ods) assays(ods)[['pValue']][1:10,1:10]