InData-class: Class "InData" ~~~

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

Description

A Class containing input data for CNA

Objects from the Class

Objects can be created by calls of the form new("InData", Chr, Pos, Test, Norm, ratio, GC).

Slots

Chr:

Object of class "character". Name of the Chromosomes/Contigs of each window.

Pos:

Object of class "numeric". Starting position of the each window.

Test:

Object of class "numeric". Number of reads from Test in each window.

Norm:

Object of class "numeric". Number of reads from Normal (Control) in each window.

ratio:

Object of class "numeric". Ratio Test/Control in each window. Automatically computed if Test and Norm are provided, or user generated if Test and Norm are not know.

GC:

Object of class "numeric". GC content of each window.

Methods

length

signature(x = "InData"): Returns number of windows from input data.

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.