estGlobParam {mBPCR} | R Documentation |
Function to estimate the global parameters of copy number data: the mean and the variance of the segment levels (called nu
and rhoSquare
, respectively), the variance of the noise (sigmaSquare
). It is possible
to choose the estimator of rhoSquare
(i.e. either \hat{rho}_1^2 or \hat{rho}^2) and by default \hat{rho}_1^2 is used.
estGlobParam(y, nu=NULL, rhoSquare=NULL, sigmaSquare=NULL, typeEstRho=1)
y |
array containing the log2ratio of the copy number data |
nu |
mean of the segment levels. If nu=NULL , then the algorithm estimates it on the sample. |
rhoSquare |
variance of the segment levels. If rhoSquare=NULL , then the algorithm estimates it on the sample. |
sigmaSquare |
variance of the noise. If sigmaSquare=NULL , then the algorithm estimates it on the sample. |
typeEstRho |
choice of the estimator of rhoSquare . If typeEstRho=1 , then the algorithm estimates rhoSquare
with \hat{rho}_1^2, if typeEstRho=0 estimates it with \hat{rho}^2. |
A list cointaining nu
, rhoSquare
and sigmaSquare
.
##import the 10K data of cell line REC ##for windows path <- 'data\\rec10k.dat' ##for linux ##path <- 'data//rec10k.dat' rec10k <- importCNData(path, NRowSkip=1) ##estimation of all the global parameters (the variance of the segment is estimated with \hat{rho}^2_1) estGlobParam(rec10k$logratio)[Package mBPCR version 1.0 Index]