aroma.core (version 2.14.0)

doCBS: Performs Circular Binary Segmentation (CBS) on a data set

Description

Performs Circular Binary Segmentation (CBS) on a data set for one or more chip types.

Usage

## S3 method for class 'default':
doCBS(dataSet, tags=NULL, chipTypes, arrays=NULL, ..., verbose=FALSE)
  ## S3 method for class 'CopyNumberDataSet':
doCBS(ds, arrays=NULL, ...)
  ## S3 method for class 'CopyNumberDataSetTuple':
doCBS(dsTuple, arrays=NULL, ..., verbose=FALSE)

Arguments

ds, dsTuple, dataSet

A CopyNumberDataSet, a CopyNumberDataSetTuple or a character string with the

tags

An optional character vector of data set tags (only when dataSet is specified).

chipTypes

A character vector specifying the chip types for the different data sets (only when dataSet is specified).

arrays

An optional vector specifying the subset of arrays to process.

...

Additional arguments passed to CbsModel and its fit() method.

verbose

A logical or Verbose.

Value

• Returns the output dataset of CbsModel.

Examples

dataSet <- "GSE20939"
tags <- "ACC,-XY,BPN,-XY,RMA,FLN,-XY"
chipTypes <- c("Mapping250K_Nsp", "Mapping250K_Sty")
fit <- doCBS(dataSet, tags=tags, chipTypes=chipTypes, verbose=-10)
print(fit)