read.exprSet {Biobase}R Documentation

Read Experimental Data and into an 'exprSet' Object

Description

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.

Usage

read.exprSet(exprs, se.exprs, phenoData, annotation, description, notes, seps = "\t")

Arguments

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

Details

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.

Value

This function returns an exprSet object.

Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide bioinformatics functionalities through R

Author(s)

Jianhua Zhang

See Also

exprSet, phenoData, MIAME, read.phenoData, read.MIAME

Examples

# 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

[Package Biobase version 1.8.0 Index]