CNAnorm-class: Class "CNAnorm"

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

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 [e-mail] and Arief Gusnanto [e-mail]

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))

Example output

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