makeGenericArray {GenomeGraphs} | R Documentation |
Creates an object of class Generic Array representing microarray data. This could be gene expression, array CGH, etc.
makeGenericArray(intensity, probeStart, probeEnd, segmentation, dp = NULL)
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 |
Object of class GenericArray
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~~further notes~~
~Make other sections like Warning with section{Warning }{....} ~
Jim Bullard and Steffen Durinck
~put references to the literature/web site here ~
~~objects to See Also as help
, ~~~
##---- 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) }