read.AnnotatedDataFrame: Read and write 'AnnotatedDataFrame'
In Biobase: Biobase: Base functions for Bioconductor

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/methods-AnnotatedDataFrame.R

Create an instance of class AnnotatedDataFrame by reading a file, or save an AnnotatedDataFrame to a file.

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="")

`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`

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.

read.AnnotatedDataFrame: An instance of class AnnotatedDataFrame

write.AnnotatedDataFrame: NULL, invisibly.

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

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

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