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.

### See Also

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

### 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 2.52.0 Index]