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Last data update: 2014.03.03

R: The constructor for the cghMCR class

cghMCR

R Documentation

The constructor for the cghMCR class

Description

Instantiates a cghMCR object using the parameters passed.

Usage

cghMCR(segments, gapAllowed = 500, alteredLow = 0.03, alteredHigh =
0.97, spanLimit = 2e+07, recurrence = 75, thresholdType = c("quantile",
"value"))

Arguments

`segments`	`segments` is a data frame extracted from the "output" element of the object returned by segment of the package DNAcopy or `getSegments`
`gapAllowed`	`gapAllowed` is an integer specifying low threshold of base pair number to separate two adjacent segments, belower which the two segments will be joined as an altered span
`alteredLow`	`alteredLow` is a positive number between 0 and 1 specifying the lower reshold percential value. Only segments with values falling below this threshold are considered as altered span
`alteredHigh`	`alteredHigh` is a positive number between 0 and 1 specifying the upper reshold percential value. Only segments with values falling over this threshold are considered as altered span
`recurrence`	`recurrence` is an integer between 1 and 100 that specifies the rate of occurrence for a gain or loss that are observed across sample. Only gains/losses with ocurrence rate grater than the threshold values are declared as MCRs
`spanLimit`	`spanLimit` is an integer that defines the leangh of altered spans that can be considered as locus. It is not of any use at this time
`thresholdType`	`thresholdType` is a character string that can be either "quantile" or "value" indicating wether `alteredLow` or `alteredHigh` is quantial or actual value

Details

The function is just a constructor of the cghMCR class for the instantiation of a cghMCR object

Value

An object of the cghMCR class

Note

The function is a contribution of The Center for Applied Cancer Science of Dana-Farber Cancer Institute

Author(s)

Jianhua Zhang

References

References on S4 class

Examples

  data("segData")
  cghmcr <- cghMCR(segData, gapAllowed = 500,
         alteredLow = 0.20, alteredHigh = 0.80, recurrence = 50)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(cghMCR)
Loading required package: DNAcopy
Loading required package: CNTools
Loading required package: tools
Loading required package: genefilter
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cghMCR/cghMCR.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cghMCR
> ### Title: The constructor for the cghMCR class
> ### Aliases: cghMCR segData
> ### Keywords: methods
> 
> ### ** Examples
> 
>   data("segData")
>   cghmcr <- cghMCR(segData, gapAllowed = 500,
+          alteredLow = 0.20, alteredHigh = 0.80, recurrence = 50)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>