subMA: MA plot

In peterawe/CMScaller: CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

Description

Mean versus average (MA) plot of output from subDEG.

Usage

subMA(
  deg,
  geneID = "rownames",
  lfc = log2(2),
  padj = 0.01,
  ave = 1,
  topN = 10,
  cexText = 1,
  classCol = getOption("subClassCol"),
  ...
)

Arguments

deg	output from subDEG which may be either a list or data.frame.
geneID	character, column names to use for labeling top hits.
lfc	numeric absolute log2(fold-change) threshold.
padj	numeric, adjusted p-value threshold.
ave	numeric, average expression threshold. length(class)==ncol(emat).
topN	an integer, number of genes to label in plot (selected by largest absolute fold-change).
cexText	numeric, scaling factor for labels for top hits.
classCol	a character vector specifying class colors.
...	additional arguments passed to plot or smoothScatter or if KernSmooth is available (currently only main, xlab and ylab used).

Value

a MA-plot

Examples

deg <- subDEG(crcTCGAsubset, crcTCGAsubset$CMS, doVoom=TRUE, sortBy="B")
subMA(deg, geneID="symbol", lfc=3)

peterawe/CMScaller documentation built on June 13, 2020, 4:49 a.m.