degPerContrast: Base mean threshold

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Base mean threshold

Description

Base mean threshold

Usage

degPerContrast(object, ...)

## S4 method for signature 'DESeqAnalysis'
degPerContrast(
  object,
  i = NULL,
  direction = c("both", "up", "down"),
  return = c("matrix", "list")
)

Arguments

object	Object.
i	character, numeric, or NULL. Names or range of results. If set NULL, include all results.
direction	character(1). Include "both", "up", or "down" directions.
return	character(1). Return type. Uses match.arg() internally and defaults to the first argument in the character vector.
...	Additional arguments.

Value

• matrix: Matrix containing numbers of DEGs per contrast. Intended primarily for use with plotDegStackedBar().

• list: Named vector containing the DEG identifiers. Intended primarily for use with plotDegUpset().

Note

Updated 2022-05-18.

Examples

data(deseq)

## DESeqAnalysis ====
degPerContrast(deseq)

steinbaugh/DESeqAnalysis documentation built on June 9, 2025, 7:56 a.m.