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]