biobroom (version 1.4.2)

ExpressionSet_tidiers: Tidying methods for Biobase's ExpressionSet objects

Description

Tidying methods for Biobase's ExpressionSet objects

Usage

"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)

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

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

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)