Params-class {CNAnorm} | R Documentation

## Class "Params"

### Description

A Class containing some Parameters used in the analysis. Not heavily used at the moment.

### Objects from the Class

Objects can be created by calls of the form `new("Params")`, it is usually iniziated and populated with methods and functions of class `CNAnorm`.

### Slots

`method`:

  variable of class `"character"`. Record if the `peakPloidy` function was called using `density` or `mixture`.

`density.n`:

  The variable `"n"` used when calling `peakPloidy`. This variable is saved so that can be used later for drawing plots.

`density.adjust`:

  The variable `"adjust"` used when calling `peakPloidy`. This variable is saved so that can be used later for drawing plots

`gc.excludeFromGCNorm`:

  Vector of class `"character"`. Name of the Chromosomes/Contigs not used for GC content correction.

`gc.maxNumPoints`:

  One element vector of class `"numeric"`. Specify how many points to use for GC correction

`gp.excludeFromDensity`:

  Vector of class `"character"`. Name of the Chromosomes/Contigs not used for peak guessing

### Methods

length

  `signature(x = "Params")`

### Author(s)

Stefano Berri

### References

Gusnanto, A., Wood, H.M., Pawitan, Y., Rabbitts, P. and Berri, S. (2011) Correcting for cancer genome size and tumor cell content enables better estimation of copy number alterations from next generation sequence data. Bioinformatics

### See Also

`CNAnorm`

### Examples

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

[Package CNAnorm version 1.38.0 Index]