aberrant: Number of aberrant events

aberrantR Documentation

Number of aberrant events

Description

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

Usage

aberrant(object, ...)

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

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).

subsetName

The name of a subset of genes of interest for which FDR corected pvalues have been previously computed. Those FDR values on the subset will then be used to determine aberrant status. Default is NULL (using transcriptome-wide FDR corrected pvalues).

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

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 May 17, 2023, 3:51 p.m.