Read and write 'AnnotatedDataFrame'
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 |
path |
(optional) directory in which to find |
row.names |
this argument gets passed on to
|
varMetadata.char |
lines beginning with this character are used
for the |
sep, header, quote, stringsAsFactors, ... |
further arguments
that get passed on to |
widget |
logical. Currently this is not implemented, and
setting this option to |
sampleNames |
optional argument that could be used in conjunction
with |
append, fileEncoding |
Arguments as described in
|
.
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 defaultPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.