alphaSummary: Alpha level cutoff summary statistics

Description Usage Arguments Details Value Note Author(s) See Also Examples

Description

Quickly generate a summary table of various alpha level cutoffs.

Usage

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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
)

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

Arguments

object

Object.

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.

...

Additional arguments.

Details

Use either contrast or name to specify the desired contrast.

Value

integer matrix.

Note

Updated 2019-08-20.

Author(s)

Michael Steinbaugh, Lorena Patano

See Also

Examples

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data(deseq)

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

steinbaugh/DESeqAnalysis documentation built on Sept. 18, 2020, 9:27 p.m.