CNAnorm (version 1.18.0)

addDNACopy: Methods for Function addDNACopy in Package `CNAnorm'

Description

addSmooth segment ratio values in Package `CNAnorm' using DNACopy

Usage

"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

Value

"CNAnorm"

Methods

signature(object = "CNAnorm")

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

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.

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)