Differentially expressed genes

# S4 method for DESeqResults
deg(object, alpha = NULL, lfcThreshold = NULL,
  direction = c("both", "up", "down"))

# S4 method for DESeqAnalysis
deg(object, results, direction = c("both",
  "up", "down"))

Arguments

object

Object.

alpha

numeric(1). Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.

lfcThreshold

numeric(1). Log fold change ratio (base 2) cutoff threshold. If left NULL, will use the cutoff defined in the object.

direction

character(1). Plot "both", "up", or "down" directions.

results

character(1) or integer(1). Name or position of DESeqResults.

Value

character. Gene identifiers.

Examples

data(deseq) ## DESeqAnalysis ==== x <- deg(deseq, results = 1L)
#> DESeqResults: condition B vs A (shrunken LFC)
#> 171 differentially expressed genes detected.
head(x)
#> [1] "gene427" "gene419" "gene095" "gene334" "gene323" "gene494"