class.cghSeg: Class to contain and describe segmented array comparative...

In tgac-vumc/CGHbase: CGHbase: Base functions and classes for arrayCGH data analysis.

Description

Container for aCGH data and experimental metadata. cghSeg class is derived from eSet, and requires a matrix named copynumber as well as a matrix named segmented as assayData members of equal dimensions. Furthermore, columns named Chromosome, Start, and End are required as featureData members, containing feature position information.

Extends

Directly extends class eSet.

Creating Objects

new('cghSeg', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], copynumber = [matrix], segmented = [matrix], featureData = [AnnotatedDataFrame], ...)

An object of class cghSeg is generally obtained as output from segmentData.

Slots

Inherited from eSet:

assayData:

Contains matrices with equal dimensions, and with column number equal to nrow(phenoData). assayData must contain matrices copynumber and segmented with rows represening array probes and columns representing samples. Additional matrices of identical size (e.g., representing measurement errors) may also be included in assayData. Class:AssayData-class

phenoData:

See eSet

featureData:

An AnnotatedDataFrame with columns Chromosome, Start, and End containing array element position data.

experimentData:

See eSet

annotation:

See eSet

Methods

Class-specific methods.

copynumber(cghSeg), copynumber(cghSeg,matrix)<-

Access and set elements named copynumber in the AssayData-class slot.

segmented(cghSeg), segmented(cghSeg,matrix)<-

Access and set elements named segmented in the AssayData-class slot.

chromosomes, bpstart, bpend

Access the chromosomal positions stored in featureData

plot

Create a plot containing log2ratios and segments ordered by chromosomal position. TWO EXTRA OPTIONS PLUS DEFAULTS: dotres=10. Every dotres-th log2-ratio is plotted. dotres=1 plots all data. However, higher values save a lot of space and allow quicker browsing of the plots. ylimit=c(-2,5): limits of the y-axis

See eSet for derived methods.

Author(s)

Sjoerd Vosse

See Also

eSet-class, cghRaw-class, cghCall-class

Examples

# create an instance of cghSeg
new("cghSeg")

# create an instance of cghSeg through \code{segmentData}
## Not run: 
   data(Wilting)
   rawcgh <- make_cghSeg(Wilting)
   normalized <- normalize(rawcgh)
   segmented <- segmentData(normalized)

   # plot the first sample. Default only every 10th log2-ratio is plotted (dotres=10). Adjust using dotres= option below. 
   plot(segmented[,1])
   # first three chromosomes
   plot(segmented[chromosomes(segmented)<=3,1])

   # get the copynumber values of the third and fourth sample
   log2ratios <- copynumber(segmented[,3:4])

   # get the names of the samples
   sampleNames(segmented)

   # get the names of the array elements
   featureNames(segmented)

## End(Not run)

tgac-vumc/CGHbase documentation built on May 31, 2019, 8:59 a.m.