aberrant: Number of aberrant events

Description Usage Arguments Value Examples

Description

Identifies the aberrant events and returns the number of aberrant counts per gene or sample or returns a matrix indicating aberrant events.

Usage

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aberrant(object, ...)

## S4 method for signature 'OutriderDataSet'
aberrant(
  object,
  padjCutoff = 0.05,
  zScoreCutoff = 0,
  by = c("none", "sample", "gene")
)

Arguments

object

An OutriderDataSet object

...

Currently not in use.

padjCutoff

The padjust cutoff

zScoreCutoff

The absolute Z-score cutoff, if NA or NULL no Z-score cutoff is used

by

if the results should be summarized by 'sample', 'gene' or not at all (default).

Value

The number of aberrent events by gene or sample or a TRUE/FALSE matrix of the size sample x gene of aberrent events.

Examples

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ods <- makeExampleOutriderDataSet()
ods <- OUTRIDER(ods, implementation='pca')

aberrant(ods)[1:10,1:10]
tail(sort(aberrant(ods, by="sample")))
tail(sort(aberrant(ods, by="gene")))

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