read.AnnotatedDataFrame: Read 'AnnotatedDataFrame'

Description

Create an instance of class AnnotatedDataFrame by reading a file.

Usage

read.AnnotatedDataFrame(filename, path, sep = "\t", header = TRUE, quote = "", stringsAsFactors = FALSE,  row.names = 1L, varMetadata.char="#", widget = getOption("BioC")$Base$use.widgets, sampleNames = character(0), ...)

Arguments

filename

file or connection from which to read.

path

(optional) directory in which to find filename.

row.names

this argument gets passed on to read.table and will be used for the row names of the phenoData slot.

varMetadata.char

lines beginning with this character are used for the varMetadata slot. See examples.

sep, header, quote, stringsAsFactors, ...

further arguments that get passed on to read.table.

widget

logical. Currently this is not implemented, and setting this option to TRUE will result in an error. In a precursor of this function, read.phenoData, this option could be used to open an interactive GUI widget for entering the data.

sampleNames

optional argument that could be used in conjunction with widget; do not use.

Value

An instance of class AnnotatedDataFrame

Details

The function read.table is used to read pData. The argument varMetadata.char is passed on to that function as its argument comment.char. Lines beginning with varMetadata.char are expected to contain further information on the column headers of pData. The format is of the form:

# variable: textual explanation of the
    variable, units, measurement method, etc.

(assuming that # is the value of varMetadata.char). See also examples.

Examples

Run this code


exampleFile = system.file("extdata", "pData.txt", package="Biobase")

adf <- read.AnnotatedDataFrame(exampleFile)
adf
head(pData(adf))
head(noquote(readLines(exampleFile)), 11)