biobroom (version 1.4.2)

MSnSet_tidiers: Tidying methods for Biobase's ExpressionSet objects

Description

Tidying methods for Biobase's ExpressionSet objects

Usage

"tidy"(x, addPheno = FALSE, ...)

Arguments

x

MSnSet object

addPheno

whether columns should be included in the tidied output for those in the MSnSet's phenoData

...

extra arguments (not used)

Value

tidy returns a data frame with one row per gene-sample combination, with columns

protein

protein name

sample

sample name (from column names)

value

protein quantitation data

Details

addPheno=TRUE adds columns that are redundant (since they add per-sample information to a per-sample-per-gene data frame), but that are useful for some kinds of graphs and analyses.

Examples

if (require("MSnbase")) {
  library(MSnbase)
  # import MSnSet object
  data(msnset)

  # Use tidy to extract genes, sample ids and measured value
  tidy(msnset)
  # add phenoType data
  tidy(msnset, addPheno=TRUE)
}