macat (version 1.46.0)

preprocessedLoader: Read in data and produce MACAT list

Description

This function reads expression data either from a saved R-file (.RData,.rda), or from a tab-separated text-file (.xls). For building a MACAT-list structure from objects in your workspace, you can either use this function or the convenience wrapper 'buildMACAT'.

Usage

preprocessedLoader(rdatafile, chip, labels = NULL, chromLocObj = NULL,
rdafile = TRUE, tabfile = FALSE, labelfile = FALSE)

Arguments

rdatafile

Complete name of the expression data file, or the expression matrix

chip

Identifier of the used microarray. To date only commercial Affymetrix microarrays are supported by MACAT

labels

Classlabels of the samples, vector of same length as number of columns in expression matrix; alternatively complete name of textfile with one label per line

chromLocObj

Object of class chromLocation specifying the genomic position, each probe on the array is mapped to. If not provided, it is build in the function using annotate's function buildChromLocation.

rdafile

Logical; is first argument a saved R-file?

tabfile

Logical; is first argument a tab-separated text file?

labelfile

Logical; is third argument a file with one label per line?

Value

List of class 'MACATData' with 6 components:

geneName

Identifiers of genes/probe sets in expression data

geneLocation

Location of genes on their chromosome as distance from 5'end in base pairs Negative numbers denote genes on the antisense strand.

chromosome

Chromosome of the respective gene. Components 'geneName', 'geneLocation', and 'chromosome' are in the same order.

expr

expression matrix with rows = genes and columns = samples/patients

labels

(disease) subtype of each sample, has length = number of columns of expression matrix

chip

Identifier for Microarray used for the experiments

See Also

buildMACAT,read.table, stjd,stjude in package 'stjudem'

Examples

 ## Not run: 
#   # assume you have your HG-U95Av2 expression values in a
#   # tab-separated text file, called 'foo.txt'
#   mydata <- preprocessedLoader("foo.txt","hgu95av2",rdafile=FALSE,tabfile=TRUE)
#  ## End(Not run)