alphaSummary: Alpha level cutoff summary statistics

alphaSummaryR Documentation

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:

  1. Name of factor in the design formula.

  2. Name of numerator level for the fold change.

  3. 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 2022-05-17.

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")

steinbaugh/DESeqAnalysis documentation built on June 25, 2022, 7:29 a.m.