MSnSet_tidiers: Tidying methods for Biobase's ExpressionSet objects
In StoreyLab/biobroom: Turn Bioconductor objects into tidy data frames

Description Usage Arguments Details Value Examples

Tidying methods for Biobase's ExpressionSet objects

1 2	## S3 method for class 'MSnSet' tidy(x, addPheno = FALSE, ...)

`x`	MSnSet object
`addPheno`	whether columns should be included in the tidied output for those in the MSnSet's phenoData
`...`	extra arguments (not used)

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.

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

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)
}