ExpressionSet_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 'ExpressionSet'
tidy(x, addPheno = FALSE,
  assay = Biobase::assayDataElementNames(x)[1L], ...)

Arguments

x	ExpressionSet object
addPheno	whether columns should be included in the tidied output for those in the ExpressionSet's phenoData
assay	The name of the assayDataElement to use as the values to tidy. Defaults to assayDataElementNames(x)[1L], which is usually equivalent to exprs(x).
...	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

gene	gene name
sample	sample name (from column names)
value	expressions on log2 scale

Examples

library(Biobase)
# import ExpressionSet object
data(hammer)

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

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