destiny (version 2.0.4)

ExpressionSet helpers: Convert object to

Description

These functions present quick waya to create ExpressionSet objects.

Usage

as.ExpressionSet(x, ...)
# S4 method for 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.

Value

an ExpressionSet object

Details

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

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