Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/methods-ExpressionSet.R
Create an instance of class ExpressionSet by reading data from files. ‘widget’ functionality is not implemented for readExpressionSet.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | 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. |
phenoDataFile |
(character) File or connection from which to read
phenotypic data. |
experimentDataFile |
(character) File or connection from which to read
experiment data. |
notesFile |
(character) File or connection from which to read notes;
|
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
|
phenoDataArgs |
A list of arguments to be used (with
|
experimentDataArgs |
A list of arguments to be used (with
|
sep, header, quote, stringsAsFactors, row.names |
arguments used
by the |
widget |
A boolean value indicating whether widgets can be
used. Widgets are NOT yet implemented for
|
... |
Further arguments that can be passed on to the
|
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.
1 2 3 4 5 6 | 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
|
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