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{ρ}_1^2 or \hat{ρ}^2) and by default \hat{ρ}_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 |
rhoSquare |
variance of the segment levels. If |
sigmaSquare |
variance of the noise. If |
typeEstRho |
choice of the estimator of |
A list containing:
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Rancoita, P. M. V., Hutter, M., Bertoni, F., Kwee, I. (2009). Bayesian DNA copy number analysis. BMC Bioinformatics 10: 10. http://www.idsia.ch/~paola/mBPCR
##import the 10K data of cell line REC data(rec10k) ##estimation of all the global parameters (the variance of the segment is ##estimated with \eqn{\hat{\rho}^2_1}) estGlobParam(rec10k$log2ratio)