results: Accessor function for the 'results' object in an...

Description Usage Arguments Value Examples

Description

This function assembles a results table of significant outlier events based on the given filter criteria. The table contains various information accumulated over the analysis pipeline.

Usage

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results(object, ...)

## S4 method for signature 'OutriderDataSet'
results(
  object,
  padjCutoff = 0.05,
  zScoreCutoff = 0,
  round = 2,
  all = FALSE,
  ...
)

Arguments

object

An OutriderDataSet object

...

Additional arguments, currently not used

padjCutoff

The significant threshold to be applied

zScoreCutoff

If provided additionally a z score threshold is applied

round

Can be TRUE, defaults to 2, or an integer used for rounding with round to make the output more user friendly

all

By default FALSE, only significant read counts are listed in the results. If TRUE all results are assembled resulting in a data.table of length samples x genes

Value

A data.table where each row is an outlier event and the columns contain additional information about this event. Eg padj, l2fc

Examples

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ods <- makeExampleOutriderDataSet()

ods <- OUTRIDER(ods)

res <- results(ods, all=TRUE)
res

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