ratio-methods: Methods for Function ratio in Package 'CNAnorm'

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

Description

ratio returns the Test/Normal ratio from an object of class CNAnorm. ratio is corrected for GC content if gcNorm was called.

ratio.n returns the Test/Normal normalized ratio from an object of class CNAnorm after normalization. Its input is ratio(object)

ratio.s returns the Test/Normal smoothed ratio from an object of class CNAnorm Its input is ratio(object)

ratio.s.n returns the Test/Normal smoothed and normalized ratio from an object of class CNAnorm. Its input is ratio.s(object)

segMean returns the mean of the segments as produced by DNACopy

segMean.n returns the normalized mean of the segments

Usage

ratio(object)
ratio.n(object)
ratio.s(object)
ratio.s.n(object)
segMean(object)
segMean.n(object)

Arguments

object

An object of Class "CNAnorm"

Value

A numeric vector

Author(s)

Stefano Berri <[e-mail]>

See Also

gcNorm, CNAnorm-class, DNAcopy

Examples

data(LS041)
CN <- dataFrame2object(LS041)
ratio.original <- ratio(CN)
CN.gcNorm <- gcNorm(CN, exclude = c("chrX", "chrY", "chrM"))
ratio.gc.corrected <- ratio(CN.gcNorm)

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