removeBreakpoints {GLAD} | R Documentation

## Remove breakpoints

### Description

This function optimizes the number of breakpoints.

### Usage

    removeBreakpoints.profileChr(profileChr, lambda=10, type="tricubic", param=c(d=6), verbose=FALSE, ...)
    removeLevel.profileChr <- function(profileChr, lambda=10, ...)

### Arguments

`profileChr` | Object of class `profileChr`.
`lambda` | Penalty term (λ') used during the "Optimization of the number of breakpoints" step.
`type` | Type of kernel used in the penalty term.
`param` | Parameter for the kernel used in the penalty term.
`verbose` | If `TRUE` some information are printed
`...` | Argument to be passed to `detectOutliers`, typically `alpha`.

### Details

The function `removeBreakpoints` uses the results of `chrBreakpoints` and optimizes the number of breakpoints previously detected: when a breakpoint is removed, then it is flagged out by -1 in the vector `Breakpoints` of the data.frame attribute of the object of class `profileChr`. `removeBreakpoints` is used within the global function `glad`.

### Value

Data frame.

### Author(s)

Philippe Hupé, Philippe.Hupe@curie.fr.

### See Also

`chrBreakpoints`,`glad`, `kernelpen`.

[Package GLAD version 1.0.1 Index]