results: Results

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Results

Description

Results

Usage

results(object, ...)

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

## S4 method for signature '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().

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.

Note

Updated 2022-08-30.

Examples

data(deseq)

## DESeqAnalysis ====
x <- results(deseq, i = 1L)
class(x)
colnames(x)

steinbaugh/DESeqAnalysis documentation built on April 1, 2024, 8:30 a.m.