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]