alphaSummary: Alpha Level Cutoff Summary Statistics

In roryk/bcbioRnaseq: RNA-Seq Utilities

Description

Alpha Level Cutoff Summary Statistics

Usage

alphaSummary(object, ...)

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

## S4 method for signature 'bcbioRNASeq'
alphaSummary(object, alpha = c(0.1, 0.05, 0.01, 0.001,
  1e-06), caption = NULL, ...)

Arguments

object	Object.
...	Optional. Passthrough arguments to DESeq2::results(). Use either contrast or name arguments to define the desired contrast.
alpha	Numeric vector of multiple alpha cutoffs.
caption	Optional. Character string to use as a caption.

Value

kable.

Note

bcbioRNASeq class does currently support contrast definitions, since the object contains an internal DESeqDataSet with an empty design formula.

Author(s)

Michael Steinbaugh, Lorena Patano

See Also

DESeq2::results().

Other Differential Expression Functions: contrastName, plotDEGHeatmap, plotDEGPCA, plotMeanAverage, plotVolcano, resultsTables

Examples

# bcbioRNASeq ====
alphaSummary(bcb_small)

# DESeqDataSet ====
resultsNames(dds_small)
alphaSummary(dds_small, contrast = c("treatment", "folic_acid", "control"))
alphaSummary(dds_small, name = "treatment_folic_acid_vs_control")

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.