RCPA (version 0.2.6)

plotMA: Plot MA plot from DE analysis results

Description

Plot MA plot from DE analysis results

Usage

plotMA(
  DEResult,
  pThreshold = 0.05,
  useFDR = TRUE,
  logFCThreshold = 1,
  labels = NULL,
  fitMethod = "loess"
)

Value

A ggplot object.

Arguments

DEResult

A data frame with DE analysis results. The columns are ID, p.value, pFDR, logFC, and aveExpr.

pThreshold

The p-value threshold to color significant points.

useFDR

Use FDR instead of p-value for significance.

logFCThreshold

The log2 fold change threshold to color significant points.

labels

named vector of labels to use for points, e.g., c("gene1" = "Gene 1", "gene2" = "Gene 2")

fitMethod

The method to use for fitting the loess line. If NULL then no line is drawn.

Examples

# \donttest{
library(RCPA)
library(SummarizedExperiment)

RNASeqDEExperiment <- loadData("RNASeqDEExperiment")

plotObj <- RCPA::plotMA(rowData(RNASeqDEExperiment), logFCThreshold = 0.5) + 
ggtitle("RNASeq - GSE153873")

# }