CNAnorm-class {CNAnorm} | R Documentation

## Class "CNAnorm"

### Description

Class to Contain and Describe copy number aberration (CNA) data from low coverage (approx 0.01 - 0.5X) Next Generation Sequencing

### Objects from the Class

Objects can be created by calls of the form `new("CNAnorm", InData)`.

### Slots

`InData`:

  Object of class `"InData"`. Contains input data provided by the user. All slots have same length. Each element describe one window. See Class `"InData"`

`DerivData`:

  Object of class `"DerivData"`. Contains data derived from `"InData"`. It can be Retrieved by the user, but methods should be used to populate `"DerivData"`. All slots have same length as input data. See Class DerivData

`Res`:

  Object of class `"Res"`. Contains slots with obtained results. See Class `"Res"`

`Params`:

  Object of class `"Params"`. Contains crucial parameters passed to some of the methods for reusing in later steps or for documentation.

### Methods

Summary of methods for class `"CNAnorm"`. Type `"methods ? methodName"` for more details about methodName.

chrs

  `signature(object = "CNAnorm")`: Retrieve Chromosomes/contig name

chrs<-

  `signature(object = "CNAnorm")`: Set Chromosomes/contig name

guessPeaksAndPloidy

  `signature(object = "CNAnorm")`: Estimate ploidy of the sample, tumor content and other results saved in Slot `"Res"`

length

  `signature(x = "CNAnorm")`: Returns number of element/windows

[

  `signature(x = "CNAnorm")`: Produce on object of class `"CNAnorm"` with a subser of windows

plotGenome

  `signature(object = "CNAnorm")`: Plot annotated normalized genome copy number

plotPeaks

  `signature(object = "CNAnorm")`: Plot peaks and estimated/validated ploidy

pos

  `signature(object = "CNAnorm")`: Retrieve Chromosomes/contig position

pos<-

  `signature(object = "CNAnorm")`: Set Chromosomes/contig position

ratio

  `signature(object = "CNAnorm")`: Retrieve ratio (Test/Control). If gcNorm was called, ratio is GC normalized

ratio.n

  `signature(object = "CNAnorm")`: Retrieve normalized ratio (not smoothed)

ratio.s

  `signature(object = "CNAnorm")`: Retrieve smoothed ratio

ratio.n.s

  `signature(object = "CNAnorm")`: Retrieve normalized smoothed ratio

segMean

  `signature(object = "CNAnorm")`: Retrieve segmented ratio (as provided by DNAcopy)

segMean.n

  `signature(object = "CNAnorm")`: Retrieve normalized segmented ratio

### Author(s)

Stefano Berri s.berri@leeds.ac.uk and Arief Gusnanto a.gusnanto@leeds.ac.uk

### References

CNA-norm: Discrete Normalization of Copy Number Alteration data from clinical samples (in preparation)

### See Also

`InData`, `DerivData` for documentation on the slots.

### Examples

    data(LS041)
    CNA <- new("CNAnorm", InData = new("InData", Chr = as.character(LS041$Chr), Pos = LS041$Pos,
        Test = LS041$Test, Norm = LS041$Norm, GC = LS041$GC))

[Package CNAnorm version 1.36.0 Index]