ExpressionSet-helpers: Convert object to ExpressionSet or read it from a file

In theislab/destiny: Creates diffusion maps

Convert object to ExpressionSet or read it from a file

Description

These functions present quick way to create ExpressionSet objects.

Usage

as.ExpressionSet(x, ...)

## S4 method for signature 'data.frame'
as.ExpressionSet(x, annotation_cols = !sapply(x, is.double))

read.ExpressionSet(file, header = TRUE, ...)

Arguments

x	data.frame to convert to an ExpressionSet.
...	Additional parameters to read.table
annotation_cols	The data.frame columns used as annotations. All others are used as expressions. (Logical, character or numerical index array)
file	File path to read ASCII data from
header	Specifies if the file has a header row.

Details

They work by using all continuous (double) columns as expression data, and all others as observation annotations.

Value

an ExpressionSet object

See Also

read.table on which read.ExpressionSet is based, and ExpressionSet.

Examples

library(Biobase)
df <- data.frame(Time  = seq_len(3), #integer column
                 Actb  = c(0.05, 0.3, 0.8),
                 Gapdh = c(0.2, 0.03, 0.1))
set <- as.ExpressionSet(df)
rownames(exprs(set)) == c('Actb', 'Gapdh')
phenoData(set)$Time == 1:3

theislab/destiny documentation built on Nov. 19, 2024, 5:43 a.m.