Class to contain and describe array comparative genomic hybridization regions data.
Container for aCGH regions data and experimental
cghRegions class is derived from
eSet, and requires a matrix named
assayData member. Furthermore, columns named
Avedist are required as featureData members, containing region
and position information.
Directly extends class
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
regions = [matrix],
featureData = [AnnotatedDataFrame],
An object of this class is generally obtained by running the function
Contains matrices with equal dimensions, and with column number equal to
assayDatamust contain a matrix
regionswith rows represening regions and columns representing samples. Additional matrices of identical size (e.g., representing measurement errors) may also be included in
Avedistcontaining region and position information.
Access and set elements named
Access the region and position information stored in
Create a plot displaying chromosomes on the Y-axis and base pair position on the X-axis. A new region is displayed by a slight jump with respect to the previous region. Each region is displayed as a bi-colored segment, the lower and upper part of which correspond to the proportions pl and pg of samples with a loss (red) or gain (green), respectively. The color coding is displayed as well: 1: pl (pg) < 10%; 2: 10% = pl (pg) < 30%; 3:30% = pl (pg) < 50%; 4: pl (pg) = 50%.
Create a frequency plot
eSet for derived methods. Annotation functionality is not yet supported.
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# create an instance of cghRegions new("cghRegions") # load an instance of cghRegions data(WiltingRegions) # plot all region data plot(WiltingRegions) # make a frequency plot frequencyPlot(WiltingRegions) # extract the region values values <- regions(WiltingRegions) # get the names of the samples sampleNames(WiltingRegions)