DGEobj.utils (version 1.0.6)

runEdgeRNorm: Run edgeR normalization on DGEobj

Description

Takes a DGEobj and adds a normalized DGEList object representing the result of edgeR normalization (calcNormFactors).

Usage

runEdgeRNorm(
  dgeObj,
  normMethod = "TMM",
  itemName = "DGEList",
  includePlot = FALSE,
  plotLabels = NULL
)

Arguments

dgeObj

A DGEobj containing counts, design data, and gene annotation.

normMethod

One of "TMM", "RLE", "upperquartile", or "none". (Default = "TMM")

itemName

optional string represents the name of the new DGEList. It must be unique and not exist in the passed DGEobj (Default = "DGEList")

includePlot

Enable returning a "canvasXpress" or "ggplot" bar plot of the norm.factors produced (Default = FALSE). Possible values to pass:

• FALSE or NULL: Disable plot

• TRUE or "canvasXpress": returns "canvasXpress" bar plot of the norm.factors produced.

• "ggplot": returns "ggplot" bar plot of the norm.factors produced.

plotLabels

Sample text labels for the plot. Length must equal the number of samples. (Default = NULL; sample number will be displayed)

Value

A DGEobj with a normalized DGEList added or a list containing the normalized DGEobj and a plot

Examples

# NOT RUN {
   # NOTE: Requires the edgeR package

   myDGEobj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
   myDGEobj <- DGEobj::resetDGEobj(myDGEobj)

   # Default TMM normalization
   myDGEobj <- runEdgeRNorm(myDGEobj)

   # With some options and plot output
   require(canvasXpress)
   myDGEobj <- DGEobj::resetDGEobj(myDGEobj)
   obj_plus_plot <- runEdgeRNorm(myDGEobj,
                                 normMethod = "upperquartile",
                                 includePlot = TRUE)
   myDGEobj <- obj_plus_plot[[1]]
   obj_plus_plot[[2]]
# }
# NOT RUN {
# }