MSnSet_tidiers: Tidying methods for Biobase's ExpressionSet objects

In biobroom: Turn Bioconductor objects into tidy data frames

Description

Tidying methods for Biobase's ExpressionSet objects

Usage

## S3 method for class 'MSnSet'
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

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)
}

Example output

Loading required package: broom
Loading required package: MSnbase
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'MSnbase'

biobroom documentation built on Nov. 8, 2020, 5:20 p.m.