Create MA plot

Source: R/make_MA.R

Create a scatter plot of log2 fold changes vs the mean expression signal.

make_MA(data, fdr = 0.05, label.rectangle = FALSE, top = 0,
  select.method = c("padj", "logfc"), main = NULL)

Arguments

data

matrix or data.frame with the columns for average gene expression, adjusted P-value, and log fold change; created as part of edger_analysis, limma_voom_analysis, or deseq2_analysis.
fdr

numerical value between 0 and 1 indicating the threshold false discovery rate for discovering differentially expressed genes. [DEFAULT = 0.05]
label.rectangle

logical indicating whether to add rectangles underneath gene names [DEFAULT = FALSE]
top

integer indicating the number of genes to label
select.method

Character string identifying the method of selecting the top genes. One of padj or logfc
main

character string giving the plot main title

Value

A ggplot2 object