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

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

Description

addSmooth segment ratio values in Package ‘CNAnorm’ using DNACopy

Usage

## S4 method for signature 'CNAnorm'
addDNACopy(object, independent.arms = FALSE, ideograms = NULL, 
    DNAcopy.smooth = list(), DNAcopy.weight = character(), DNAcopy.segment = list())

Arguments

object	An object of Class "CNAnorm"
independent.arms	Boolean. If TRUE chromosomes arms will be treated as independent, ideograms must be provided
ideograms	A data frame containing information about banding. See ?hg19_hs_ideogr for more information
DNAcopy.smooth	A list of parameters to be passed to function 'smooth.CNA' in package DNAcopy
DNAcopy.weight	A character value of one of these values. 'poisson', 'gaussian', 'twoTailQuantile', 'oneTailQuantile'. It specifies a way to give weight to each window depending on how much coverage in the normal deviates from the median for that chromosome. Options are listed in decreasing order of stringency. See Details
DNAcopy.segment	A list of parameters to be passed to function 'segment' in package DNAcopy. Parameters 'weights' and 'verbose' are not accepted

Details

'poisson': windows with coverage more or less than 2*sqrt(mean) from the mean are weighted down. The most stringent. Recommended for unbiased genome wide sequencing.

'gaussian': windows with coverage more or less than 2*sd from the median are weighted down. Recommended for genome wide sequencing where coverage in the normal is far from poisson distribution.

'twoTailQuantile': windows with coverage outside 5-95th quantile are weighted down. Recommended when coverage is far from a normal distribution - such as capture experiments -

'oneTailQuantile': windows with coverage lower than 5th quantile are weighted down. Recommended when coverage is far from a normal distribution - such as capture experiments. Does not weight down windows with very high coverage.

Value

An object of class "CNAnorm"

Methods

signature(object = "CNAnorm")

Segment ratio values on an object of class "CNAnorm". Returns the same object with extra slots (segMean, segID )

Author(s)

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

References

Venkatraman, E. S. and Olshen, A. B. (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics

See Also

segMean, CNAnorm-class, DNAcopy, hg19_hs_ideogr

Examples

data(LS041)
CN <- dataFrame2object(LS041)
CN <- addDNACopy(CN)

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