Class to contain and describe called array comparative genomic hybridization data.

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Description

Container for aCGH data and experimental metadata. cghCall class is derived from eSet, and requires the following matrices of equal dimension as assayData members:

  • copynumber

  • segmented

  • calls

  • probloss

  • probnorm

  • probgain

Furthermore, columns named Chromosome, Start, and End are required as featureData members, containing feature position information.

Extends

Directly extends class eSet.

Creating Objects

new('cghCall', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], copynumber = [matrix], segmented = [matrix], calls = [matrix], probloss = [matrix], probnorm = [matrix], probgain = [matrix], featureData = [AnnotatedDataFrame], ...)

An object of class cghCall is generally obtained as output from CGHcall.

Slots

Inherited from eSet:

assayData:

Contains matrices with equal dimensions, and with column number equal to nrow(phenoData). assayData must contain the following matrices

  • copynumber

  • segmented

  • calls

  • probloss

  • probnorm

  • probgain

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(cghCall), copynumber(cghCall,matrix)<-

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

segmented(cghCall), segmented(cghCall,matrix)<-

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

calls(cghCall), calls(cghCall,matrix)<-

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

probloss(cghCall), probloss(cghCall,matrix)<-

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

probnorm(cghCall), probnorm(cghCall,matrix)<-

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

probgain(cghCall), probgain(cghCall,matrix)<-

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

chromosomes, bpstart, bpend

Access the chromosomal positions stored in featureData

plot

Create a plot containing log2ratios, segments and call probabilities ordered by chromosomal position. 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(-5,5): limits of the y-axis. gaincol='green'; losscol='red';ampcol="darkgreen";dlcol="darkred": Colors used for gain, loss (bars) and amplifications, double loss (tick marks). build='GRCh37': build of humun genome used for determining positions of centromeres

plot.summary

Create a plot summarizing the call probabilities of all samples

frequencyPlotCalls

Create a frequency plot summarizing the calls of all samples

See eSet for derived methods.

Author(s)

Sjoerd Vosse

See Also

eSet-class, cghRaw-class, cghSeg-class

Examples

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

# create an instance of cghCall through \code{\link{ExpandCGHcall}}
## Not run: 
   data(Wilting)
   rawcgh <- make_cghSeg(Wilting)
   normalized <- normalize(rawcgh)
   segmented <- segmentData(normalized)
   perc.tumor <- rep(0.75, 3)
   listcalled <- CGHcall(segmented,cellularity=perc.tumor)
   called <- ExpandCGHcall(listcalled,segmented)

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

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

   # get the names of the samples
   sampleNames(called)

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

## End(Not run)