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

In OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

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

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

ods <- makeExampleOutriderDataSet()

ods <- OUTRIDER(ods)

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

OUTRIDER documentation built on Nov. 8, 2020, 5:16 p.m.