preprocessedLoader {macat} | R Documentation

## 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

### Note

At present, `macat` can only work with Affymetrix microarrays, for which an annotation package is installed on your system. Such annotation packages can either be obtained from the Bioconductor annotation packages repository or be constructed using the Bioconductor package `AnnBuilder`. For an example, see the common annotation package `hgu95av2`.

### Author(s)

MACAT development team

### 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)

[Package macat version 1.14.0 Index]