Differentially expressed genes

Usage

deg(object, ...)

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

# S4 method for class '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)
#> → condition_B_vs_A (shrunken LFC)
#> ℹ 30 differentially expressed genes (alpha < 0.01).
head(x)
#> [1] "gene483" "gene262" "gene434" "gene478" "gene65"  "gene43"