resultsTables: Differential Expression Results Tables
In roryk/bcbioRnaseq: RNA-Seq Utilities

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

Differential Expression Results Tables

resultsTables(results, counts, ...)

## S4 method for signature 'DESeqResults,DESeqDataSet'
resultsTables(results, counts, alpha,
  lfcThreshold = 0L, summary = TRUE, write = FALSE, headerLevel = 2L,
  dir = ".", dropboxDir = NULL, rdsToken = NULL)

`results`	`DESeqResults` object.
`counts`	`DESeqDataSet` containing the counts that were used to generate the `DESeqResults`.
`...`	Additional arguments.
`alpha`	Adjusted P value ("alpha") cutoff.
`lfcThreshold`	Log fold change ratio (base 2) cutoff threshold.
`summary`	Show summary statistics.
`write`	Write CSV files to disk.
`headerLevel`	R Markdown header level.
`dir`	Local directory path.
`dropboxDir`	Dropbox directory path where to archive the results tables for permanent storage (e.g. Stem Cell Commons). When this option is enabled, unique links per file are generated internally with the rdrop2 package.
`rdsToken`	RDS file token to use for Dropbox authentication.

list containing modified DESeqResults return, including additional gene-level metadata and normalized counts.

Log fold change cutoff threshold ("lfcThreshold") does not apply to statistical hypothesis testing, only gene filtering in the results tables. See DESeq2::results() for additional information about using lfcThreshold and altHypothesis to set an alternative hypothesis based on expected fold changes.

Michael Steinbaugh

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

# DESeqResults, DESeqDataSet ====
x <- resultsTables(
    results = res_small,
    counts = dds_small,
    lfcThreshold = 0.25
)
names(x)
glimpse(x[["deg"]])