| read.exprSet {Biobase} | R Documentation |
An exprSet object has a slot named exprs for experimental data. read.exprSet reads the experimental data stored as a text file and then generates an exprSet object using the data. Data for other slots can be also read in as options.
read.exprSet(exprs, se.exprs, phenoData, annotation, description, notes, seps = "\t")
exprs |
exprs a character string for the name of the text
file that stores the experimental data to be read in. The text file
is assumed to be a delimited file with observed expression levels
arranged in rows and columns. The first row of the file is sample
names and the first column is gene names/ids. The file will be
read in using read.table with header set to TRUE |
se.exprs |
se.exprs a character stirng for the name of a
delimited text file contains standard error estimates for the estimated
expression in exprs. The file is of the same dimensions as
'exprs' |
phenoData |
phenoData a character string for the name of an
optional file containing information for 'pData' slot of a phenoData
object to be returned. If missing a default phenoData object with
one covariate ranging from 1 to the number of columns of 'exprs'
will be provided |
annotation |
annotation a character string for the name of
an optional text file that contains a string identifying the
annotation that may be used for the 'exprSet' instance |
description |
description a character string for the name
of an optional file containing MIAME information |
notes |
notes a character string for the name of an
optional text file containing explanatory text |
seps |
seps a vector of character strings defining the
delimitors used by 'exprs' and 'se.exprs'. The length of 'seps' can
be 1 when both file have the same delimiter or 'se.exprs' is missing
or 2 other wise. The delimitor for 'exprs' is expected to be the
first element |
If not missing, 'phenoData' will be read in using
read.phenoData and description using
read.MIAME. The help files of the two functions contain
detailed descriptions of the two functions.
This function returns an exprSet object.
This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide bioinformatics functionalities through R
Jianhua Zhang
exprSet, phenoData,
MIAME, read.phenoData,
read.MIAME
# Creating a test data testFile <- tempfile() data(geneData) write.table(geneData, testFile, quote = FALSE, sep = "\t", row.names = TRUE, col.names = TRUE) # Create an exprSet object using textFile eSet <- read.exprSet(testFile) eSet