degIntersection: Intersection of differentially expressed genes

In steinbaugh/DESeqAnalysis: DESeq2 Analysis Utilities

Description

Intersection of differentially expressed genes

Usage

degIntersection(object, ...)

## S4 method for signature 'DESeqAnalysis'
degIntersection(
  object,
  i = NULL,
  direction = c("up", "down"),
  return = c("matrix", "count", "ratio")
)

Arguments

object	Object.
i	character, numeric, or NULL. Names or range of results. If set NULL, include all results.
direction	character(1). Include "up" or "down" directions. Must be directional, and intentionally does not support "both".
return	character(1). Return intersection matrix, count per contrast, or ratio.
...	Passthrough arguments to deg().

Value

integer. Integer denoting the number of intersections, sorted from highest to lowest. Gene identifiers are defined as the names.

Note

Updated 2020-08-18.

Examples

data(deseq)

## DESeqAnalysis ====
mat <- degIntersection(deseq, return = "matrix")
head(mat)

count <- degIntersection(deseq, return = "count")
head(count)

ratio <- degIntersection(deseq, return = "ratio")
head(ratio)

steinbaugh/DESeqAnalysis documentation built on Oct. 15, 2020, 2:02 a.m.