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

To date MACAT can only work with commercial Affymetrix microarrays, denoted by one the following identifiers: hu6800, hgu95av2, hgu95b, hgu95c, hgu95d, hgu95e, hgu133a, hgu133b, mgu74av2, mgu74bv2, mgu74c, moe430a, moe430b, rae230a, rae230b, rgu34a, rgu34b, rgu34c

### 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 1.8.0 Index]