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, ...)
read.table
is called with this
as its file
argument and further arguments given by exprsArgs
.read.AnnotatedDataFrame
is called
with this as its file
argument and further arguments given by
phenoDataArgs
.read.MIAME
is called with this
as its file
argument and further arguments given by
experimentDataArgs
.readLines
is used to input the file.read.table
when reading in the expression matrix.read.AnnotatedDataFrame
) when reading
the phenotypic data.read.MIAME
) when reading the experiment data.read.table
-like functions.read.AnnotatedDataFrame
.read.table
-like functions.ExpressionSet
class.
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.
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
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