MSnSet_tidiers

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Tidying methods for Biobase's ExpressionSet objects

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)
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.

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

Aliases
  • MSnSet_tidiers
  • tidy.MSnSet
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)
}
Documentation reproduced from package biobroom, version 1.4.2, License: LGPL

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