cghRegions {CGHbase} | R Documentation |
Container for aCGH regions data and experimental
metadata. cghRegions
class is derived from
eSet
, and requires a matrix named regions
as
assayData member. Furthermore, columns named Chromosome
, Start
, End
,
Nclone
, and Avedist
are required as featureData members, containing region
and position information.
Directly extends class eSet
.
new('cghRegions',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
regions = [matrix],
featureData = [AnnotatedDataFrame],
...)
An object of this class is generally obtained by running the function CGHregions
.
Inherited from eSet
:
assayData
:Contains matrices with equal
dimensions, and with column number equal to
nrow(phenoData)
. assayData
must contain a matrix
regions
with rows represening regions
and columns representing samples. Additional matrices of
identical size (e.g., representing measurement errors) may
also be included in assayData
. Class:AssayData
phenoData
:See eSet
featureData
:An AnnotatedDataFrame
with columns
Chromosome
, Start
, End
, Nclone
, and Avedist
containing region
and position information.
experimentData
:See eSet
annotation
:See eSet
Class-specific methods.
regions(cghRegions)
, regions(cghRegions,matrix)<-
Access and
set elements named regions
in the AssayData-class
slot.
chromosomes
, bpstart
, bpend
, nclone
, avedist
Access the region and position
information stored in featureData
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
See eSet
for derived methods. Annotation functionality is not yet supported.
Sjoerd Vosse
eSet
, cghRaw-class
, cghSeg-class
, cghCall-class
# 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)