resultsTables: Results tables

In acidgenomics/r-deseqanalysis: Acid Genomics DESeq2 Analysis Utilities

Results tables

Description

Results tables

Usage

resultsTables(object, ...)

## S4 method for signature 'DESeqAnalysis'
resultsTables(
  object,
  i,
  alphaThreshold = NULL,
  baseMeanThreshold = NULL,
  lfcThreshold = NULL,
  extra = TRUE
)

## S4 method for signature 'DESeqResults'
resultsTables(
  object,
  alphaThreshold = NULL,
  baseMeanThreshold = NULL,
  lfcThreshold = NULL
)

Arguments

object	Object.
i	character(1) or integer(1). DESeqResults contrast name or position in results slot.
alphaThreshold	numeric(1) or NULL. Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.
baseMeanThreshold	numeric(1) or NULL. Base mean (i.e. average expression across all samples) threshold. If left NULL, will use the cutoff defined in the object. Applies in general to DESeq2 RNA-seq differential expression output.
lfcThreshold	numeric(1) or NULL. Log (base 2) fold change ratio cutoff threshold. If left NULL, will use the cutoff defined in the object.
extra	logical(1). Include row data (i.e. gene metadata) and normalized counts from the internal DESeqDataSet.
...	Additional arguments.

Details

Generate tables summarizing the differential expression, with subsets for differentially expressed genes (DEGs). DEG tables (i.e. everything except the all table), are arranged by adjusted P value.

Value

DFrameList. Named list containing subsets of DESeqResults.

Tables

• all: All genes, including genes without an adjusted P value. This table is unmodified, and the rows have not been re-arranged or subset. It is suitable for gene set enrichment analysis (GSEA).

• up: Upregulated genes.

• down: Downregulated genes.

• both: Bidirectional DEGs (up- and down-regulated). This table can be used for overrepresentation testing but should NOT be used for GSEA.

Note

Updated 2022-05-24.

It is generally recommended to not apply post hoc log fold change cutoffs. If a specific effect size is desired, instead run DESeq2::results() using the lfcThreshold parameter. Refer to the DESeq2 documentation and vignette for details.

Examples

data(deseq)

## DESeqAnalysis ====
x <- resultsTables(deseq, i = 1L)
print(x)

acidgenomics/r-deseqanalysis documentation built on March 30, 2024, 12:08 p.m.