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.
1 2 3 4 5 6 7 8 | 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
1 2 3 4 5 6 7 8 | 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
|
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