aberrant: Number of aberrant events

In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

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 were 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 April 29, 2024, 2:22 a.m.