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.
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