degMA: MA-plot from base means and log fold changes

In DEGreport: Report of DEG analysis

Description

MA-plot addaptation to show the shrinking effect.

Usage

degMA(
  results,
  title = NULL,
  label_points = NULL,
  label_column = "symbol",
  limit = NULL,
  diff = 5,
  raw = FALSE,
  correlation = FALSE
)

Arguments

results	DEGSet class.
title	Optional. Plot title.
label_points	Optionally label these particular points.
label_column	Match label_points to this column in the results.
limit	Absolute maximum to plot on the log2FoldChange.
diff	Minimum difference between logFoldChange before and after shrinking.
raw	Whether to plot just the unshrunken log2FC.
correlation	Whether to plot the correlation of the two logFCs.

Value

MA-plot ggplot.

Author(s)

Victor Barrera

Rory Kirchner

Lorena Pantano

Examples

library(DESeq2)
dds <- makeExampleDESeqDataSet(betaSD=1)
dds <- DESeq(dds)
res <- degComps(dds, contrast = list("condition_B_vs_A"))
degMA(res)

DEGreport documentation built on Nov. 8, 2020, 7:23 p.m.