read.AnnotatedDataFrame

Read 'AnnotatedDataFrame'

Create an instance of class AnnotatedDataFrame by reading a file.

Keywords
manip, 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.
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.

Value

An instance of class AnnotatedDataFrame

See Also

AnnotatedDataFrame for additional methods, read.table for details of reading in phenotypic data

Aliases
  • read.AnnotatedDataFrame
Examples

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

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

Documentation reproduced from package Biobase, version 2.26.0, License: Artistic-2.0

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