deg: Differentially expressed genes

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Differentially expressed genes

Description

Differentially expressed genes

Usage

deg(object, ...)

## S4 method for signature 'DESeqAnalysis'
deg(object, i, direction = c("both", "up", "down"), quiet = FALSE)

## S4 method for signature 'DESeqResults'
deg(
  object,
  direction = c("both", "up", "down"),
  alphaThreshold = NULL,
  baseMeanThreshold = NULL,
  lfcThreshold = NULL,
  quiet = FALSE
)

Arguments

object	Object.
i	Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL. For more information: help(topic = "Extract", package = "base")
direction	character(1). Include "both", "up", or "down" directions.
quiet	logical(1). Perform command quietly, suppressing messages.
alphaThreshold	numeric(1) or NULL. Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.
baseMeanThreshold	numeric(1) or NULL. Base mean (i.e. average expression across all samples) threshold. If left NULL, will use the cutoff defined in the object. Applies in general to DESeq2 RNA-seq differential expression output.
lfcThreshold	numeric(1) or NULL. Log (base 2) fold change ratio cutoff threshold. If left NULL, will use the cutoff defined in the object.
...	Additional arguments.

Value

character. Gene identifiers.

Note

Updated 2023-12-18.

Examples

data(deseq)

## DESeqAnalysis ====
x <- deg(deseq, i = 1L)
head(x)

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