callPeaks.PeaksAndValleys: Calls the peaks in peaks-and-valley estimates

In HenrikBengtsson/aroma.cn: Copy-Number Analysis of Large Microarray Data Sets

Calls the peaks in peaks-and-valley estimates

Description

Calls the peaks in peaks-and-valley estimates to a set of known state.

Usage

## S3 method for class 'PeaksAndValleys'
callPeaks(fit, expected=c(-1/2, -1/4, 0, +1/4, +1/2) * pi, flavor=c("decreasing", "all"),
  verbose=FALSE, ...)

Arguments

fit	A KxC data.frame of peaks-and-valley estimates.
expected	The expected locations of the peaks to be called.
flavor	A character string specifying what flavor of the caller to use.
verbose	A logical or a Verbose object.
...	Not used.

Value

Returns a Kx(C+2) data.frame.

Flavors

If flavor == "all", each peak is called to the state with the closest expected value. If flavor == "decreasing", the strongest peak is called to the state with the closest expected value, then the second strongest peak is called analogously to one of the remaining states, and so on.

Author(s)

Henrik Bengtsson, Pierre Neuvial

See Also

To get peaks-and-valley estimates, use findPeaksAndValleys.

HenrikBengtsson/aroma.cn documentation built on Feb. 20, 2024, 9:15 p.m.