ExpressionSet_tidiers

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Tidying methods for Biobase's ExpressionSet objects

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)
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

Aliases
  • ExpressionSet_tidiers
  • tidy.ExpressionSet
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)

Documentation reproduced from package biobroom, version 1.4.2, License: LGPL

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