Results — results • DESeqAnalysis

Results

Usage

results(object, ...)

# S4 method for class 'DESeqAnalysis'
results(object, i, lfcShrink = NULL, extra = FALSE, quiet = TRUE)

# S4 method for class 'DESeqDataSet'
results(object, ...)

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")

lfcShrink

logical(1) or NULL. Use shrunken log2 fold change (LFC) values. If NULL, inherits value defined in lfcShrink().

extra

logical(1). Include row data (i.e. gene metadata) and normalized counts from the internal DESeqDataSet.

quiet

logical(1). Perform command quietly, suppressing messages.

...

Additional arguments.

Value

DESeqResults.

Functions

results(DESeqDataSet): Arguments pass through to DESeq2::results().

Note

Updated 2023-12-18.

Extra mode

Get the DESeqDataSet, and humanize the sample names. Note that we're not calling humanize() here on the DESeqDataSet, because we want to keep the gene identifiers in the row names. Use human-friendly sample names, defined by the sampleName column in colData. We're using this downstream when joining the normalized counts.

Examples

data(deseq)

## DESeqAnalysis ====
x <- results(deseq, i = 1L)
class(x)
#> [1] "DESeqResults"
#> attr(,"package")
#> [1] "DESeq2"
colnames(x)
#> [1] "baseMean"       "log2FoldChange" "lfcSE"          "pvalue"        
#> [5] "padj"