| read.AnnotatedDataFrame {Biobase} | R Documentation |
Create an instance of class AnnotatedDataFrame by reading 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), ...)
filename |
file or connection from which to read. |
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. |
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. |
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.
An instance of class AnnotatedDataFrame
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(readLines(exampleFile))