R: Read and write 'AnnotatedDataFrame'

read.AnnotatedDataFrame {Biobase}

R Documentation

Read and write 'AnnotatedDataFrame'

Description

Create an instance of class AnnotatedDataFrame by reading a file, or save an AnnotatedDataFrame to 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), ...) 
write.AnnotatedDataFrame(x, file="", varMetadata.char="#", ...,
     append=FALSE, fileEncoding="")

Arguments

`filename, file`	file or connection from which to read / write.
`x`	An instance of class `AnnotatedDataFrame`.
`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` or `write.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.
`append, fileEncoding`	Arguments as described in `write.table`

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.

write.AnnotatedDataFrame outputs varLabels and varMetadata(x)$labelDescription as commented header lines, and pData(x) as a with write.table.

Value

read.AnnotatedDataFrame: An instance of class AnnotatedDataFrame

write.AnnotatedDataFrame: NULL, invisibly.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org> and Wolfgang Huber, based on read.phenoData by Rafael A. Irizarry.

Examples


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

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

write.AnnotatedDataFrame(adf)           # write to console by default

[Package Biobase version 2.38.0 Index]