makeGenericArray {GenomeGraphs} | R Documentation

## Creates an object of class GenericArray

### Description

Creates an object of class Generic Array representing microarray data. This could be gene expression, array CGH, etc.

### Usage

    makeGenericArray(intensity, probeStart, probeEnd, segmentation, dp = NULL)

### Arguments

`intensity` | Matrix of intensities, probes in the rows, samples in the columns
`probeStart` | Vector of start positions for the probes
`probeEnd` | Vector of end positions for probes (optional)
`segmentation` | Object of class Segmentation, needs to be added if segments should be plotted as well
`dp` | Object of class DisplayPars which handles the display parameters for plotting

### Value

Object of class GenericArray

### Warning

....

### Note

~~further notes~~

~Make other sections like Warning with section{Warning }{....} ~

### Author(s)

Jim Bullard and Steffen Durinck

### References

~put references to the literature/web site here ~

### See Also

~~objects to See Also as `help`, ~~~

### Examples

    ##---- Should be DIRECTLY executable !! ----
    ##-- ==>  Define data, use random,
    ##--    or do  help(data=index)  for the standard data sets.

    ## The function is currently defined as
    function (intensity, probeStart, probeEnd, segmentation, dp = NULL)
    {
        pt <- getClass("GenericArray")@prototype
        if (is.null(dp))
            dp <- pt@dp
        if (missing(probeEnd))
            probeEnd <- pt@probeEnd
        if (missing(segmentation))
            segmentation <- pt@segmentation
        if (missing(probeStart))
            stop("Need probeStart argument to know where to plot the data on the genome")
        new("GenericArray", intensity = intensity, probeStart = probeStart,
            probeEnd = probeEnd, dp = dp, segmentation = segmentation)
      }

[Package GenomeGraphs version 1.2.3 Index]