resultsTables: Differential Expression Results Tables

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

Description

Differential Expression Results Tables

Usage

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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)

Arguments

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.

Value

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

Note

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.

Author(s)

Michael Steinbaugh

See Also

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

Examples

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

WeiSong-bio/roryk-bcbioRNASeq documentation built on July 6, 2019, 12:02 a.m.