cghseg (version 1.0.5)

getbgoutliers: getbgoutliers

Description

Identification of outliers in the background intensity

Usage

getbgoutliers(.Object,CGHr.smooth,fdr)

Arguments

.Object

an object of the CGHresults class for which CGHo["wavenorm"]="position"

CGHr.smooth

an object of the CGHresults class for which CGHo["wavenorm"] is "spline"

fdr

fdr level to control for multiple testing

Value

bgoutliers

dataframe containing background outliers

References

Joint segmentation, calling and normalization of multiple CGH profiles, Biostatistics (2011)

Examples

# NOT RUN {
set.seed(1)
simul          = simulprofiles(M=5,n=100,k.mean=2,SNR=5,lambda=1)
CGHd           = new("CGHdata",Y=simul$Y)
CGHo           = new("CGHoptions")
calling(CGHo)  = FALSE
wavenorm(CGHo) = "position"
CGHr.pos       = multiseg(CGHd,CGHo)
wavenorm(CGHo) = "spline"
CGHr.spl       = multiseg(CGHd,CGHo)
getbgoutliers(CGHr.pos,CGHr.spl,fdr=0.05)
# }