readExpressionSet {Biobase} | R Documentation |
Create an instance of class ExpressionSet by reading data from files. ‘widget’ functionality is not implemented for readExpressionSet.
readExpressionSet(exprsFile, phenoDataFile, experimentDataFile, notesFile, path, annotation, ## arguments to read.* methods exprsArgs=list(sep=sep, header=header, row.names=row.names, quote=quote, ...), phenoDataArgs=list(sep=sep, header=header, row.names=row.names, quote=quote, stringsAsFactors=stringsAsFactors, ...), experimentDataArgs=list(sep=sep, header=header, row.names=row.names, quote=quote, stringsAsFactors=stringsAsFactors, ...), sep = "\t", header = TRUE, quote = "", stringsAsFactors = FALSE, row.names = 1L, ## widget widget = getOption("BioC")$Base$use.widgets, ...)
exprsFile |
(character) File or connection from which to read expression
values. The file should contain a matrix with rows as features and
columns as samples. read.table is called with this
as its file argument and further arguments given by exprsArgs . |
phenoDataFile |
(character) File or connection from which to read
phenotypic data. read.AnnotatedDataFrame is called
with this as its file argument and further arguments given by
phenoDataArgs . |
experimentDataFile |
(character) File or connection from which to read
experiment data. read.MIAME is called with this
as its file argument and further arguments given by
experimentDataArgs . |
notesFile |
(character) File or connection from which to read notes;
readLines is used to input the file. |
path |
(optional) directory in which to find all the above files. |
annotation |
(character) A single character string indicating the annotation associated with this ExpressionSet. |
exprsArgs |
A list of arguments to be used with
read.table when reading in the expression matrix. |
phenoDataArgs |
A list of arguments to be used (with
read.AnnotatedDataFrame ) when reading
the phenotypic data. |
experimentDataArgs |
A list of arguments to be used (with
read.MIAME ) when reading the experiment data. |
sep, header, quote, stringsAsFactors, row.names |
arguments used
by the read.table -like functions. |
widget |
A boolean value indicating whether widgets can be
used. Widgets are NOT yet implemented for
read.AnnotatedDataFrame . |
... |
Further arguments that can be passed on to the
read.table -like functions. |
Expression values are read using the read.table
function. Phenotypic data are read using the
read.AnnotatedDataFrame
function. Experiment data are
read using the read.MIAME
function. Notes are read using
the readLines
function. The return value must be a valid
ExpressionSet
. Only the exprsFile
argument is required.
An instance of the ExpressionSet
class.
Martin Morgan <mtmorgan@fhcrc.org>
ExpressionSet
for additional methods.
exprsFile = system.file("extdata", "exprsData.txt", package="Biobase") phenoFile = system.file("extdata", "pData.txt", package="Biobase") ## Read ExpressionSet with appropriate parameters obj = readExpressionSet(exprsFile, phenoFile, sep = "\t", header=TRUE) obj