resultsDiff: Relative difference of results

In acidgenomics/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Relative difference of results

Description

Relative difference of results

Usage

resultsDiff(x, y, ...)

## S4 method for signature 'DESeqAnalysis,missingOrNULL'
resultsDiff(x, y = NULL, i, j, ...)

## S4 method for signature 'DESeqResults,DESeqResults'
resultsDiff(
  x,
  y,
  col = c("log2FoldChange", "stat"),
  deg = c("no", "intersect", "union"),
  direction = c("both", "up", "down"),
  alphaThreshold = NULL,
  baseMeanThreshold = NULL,
  lfcThreshold = NULL
)

Arguments

x	Object.
y	Object.
i	Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL. For more information: help(topic = "Extract", package = "base")
j	Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL. For more information: help(topic = "Extract", package = "base")
...	Additional arguments.
col	character(1). Column to use for difference calculation (subtraction). Note that x/i represents A and y/j B in A - B calculation.
deg	character(1). "no": Return all genes, corresponding to original row names order. "intersect": Return only genes called as DE in both contrasts. "union": Return genes called as DE in either contrast.
direction	character(1). Include "both", "up", or "down" directions.
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.

Value

Named numeric. Names correspond to the features (i.e. genes) analyzed.

Functions

• resultsDiff(x = DESeqAnalysis, y = missingOrNULL): Passes arguments to DESeqResults method.

Note

Updated 2020-08-05.

Examples

data(deseq)

## DESeqAnalysis ====
diff <- resultsDiff(deseq, i = 1L, j = 2L)
head(diff)

acidgenomics/DESeqAnalysis documentation built on March 27, 2024, 10:32 p.m.