class.cghCall: Class to contain and describe called array comparative...

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

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

# 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)

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