cghMCR {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

### See Also

`cghMCR`

### Examples

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

[Package cghMCR version 1.45.0 Index]