ExpressionSet helper methods {destiny} | R Documentation

## 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

[Package destiny version 3.6.0 Index]