cghMCR-class {cghMCR} | R Documentation

## Class "cghMCR" is a S4 class for the identification of minimum common regions of gains or losses across samples

### Description

Objects of this class provides the functionalities to detecting chromosome regions that show gains or losses across differnet samples

### Objects from the Class

Objects can be created by calls of the form `new("cghMCR", ...)`. A constructor `cghMCR` may be used to instantiate object of this class

### Slots

`DNASeg`:

  Object of class `"data.frame"` containing segmentation data derived from segmentation analysis using segment

`DNAData`:

  Object of class `"data.frame"` containing raw data derived used for the segmentation analysisfrom segmentation analysis

`altered`:

  Object of class `"data.frame"` containing data for the altered regions

`gapAllowed`:

  Object of class `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`:

  Object of class `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`:

  Object of class `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`:

  Object of class `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 or losses with ocurrence rate grater than the threshold values are declared as MCRs

`spanLimit`:

  Object of class `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`:

  A character string that can be either "quantile", "value" to indicate the type of the value for recurrence

### Methods

MCR

  `signature(object = "cghMCR")`: identifies minimum common regions of gains/losses across samples

### Note

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

### Author(s)

Jianhua Zhang

### See Also

`cghMCR`

### Examples

      require("CNTools")
      data("sampleData")
      cghmcr <- cghMCR(sampleData[sampleData[, "ID"] %in%
             sample(unique(sampleData[, "ID"]), 20), ], gapAllowed = 500,
             alteredLow = 0.20, alteredHigh = 0.80, recurrence = 50)

[Package cghMCR version 1.50.0 Index]