Params-class: Class "Params"

In CNAnorm: A normalization method for Copy Number Aberration in cancer samples

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) 

CNAnorm documentation built on Nov. 8, 2020, 5:29 p.m.