alphaSummary: Alpha level cutoff summary statistics

In acidgenomics/r-deseqanalysis: Acid Genomics DESeq2 Analysis Utilities

Alpha level cutoff summary statistics

Description

Quickly generate a summary table of various alpha level cutoffs.

Usage

alphaSummary(object, ...)

## S4 method for signature 'DESeqAnalysis'
alphaSummary(object, ...)

## S4 method for signature 'DESeqDataSet'
alphaSummary(
  object,
  alpha = c(0.1, 0.05, 0.01, 0.001, 1e-06),
  contrast = NULL,
  name = NULL
)

Arguments

object	Object.
...	Additional arguments.
alpha	numeric. Multiple alpha cutoffs.
contrast	character. A character vector with exactly 3 elements: Name of factor in the design formula. Name of numerator level for the fold change. Name of denominator level for the fold change. See DESeq2::results() for details.
name	character(1). Name of the individual effect (coefficient) for building a results table. Use this argument rather than contrast for continuous variables.

Details

Use either contrast or name to specify the desired contrast.

Value

⁠integer matrix⁠.

Note

Updated 2023-09-26.

Author(s)

Michael Steinbaugh, Lorena Patano

See Also

• DESeq2::results().

• DESeq2::resultsNames().

Examples

data(deseq)

## DESeqAnalysis ====
alphaSummary(deseq, contrast = c("condition", "B", "A"))
alphaSummary(deseq, name = "condition_B_vs_A")

acidgenomics/r-deseqanalysis documentation built on April 13, 2025, 2:04 a.m.