cghCall {CGHbase} | R Documentation

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

### 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)

[Package CGHbase version 1.40.0 Index]