Preprocessing - Initialize matrix of latent states

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Description

This function takes a matrix of CGH data as the only argument and returns a crude estimate of the corresponding latent copy number states.

Usage

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InitXi(X, bounds = c(-0.5, 0.29, 0.79))

Arguments

X

Matrix of aCGH data

bounds

Vector of threshold used to estimate the latent states

Details

Given as argument a vector of threshold bounds the function simply applies the thresholding to the data and groups them into four subsets. Each subset is associated to a specific latent state.

Value

Return a matrix of estimated latent states, that could be used as input of the main function.

Author(s)

Alberto Cassese

References

Cassese A, Guindani M, Tadesse M, Falciani F, Vannucci M. A hierarchical Bayesian model for inference of copy number variants and their association to gene expression. Annals of Applied Statistics, 8(1), 148-175.
Cassese A, Guindani M, Vannucci M. A Bayesian integrative model for genetical genomics with spatially informed variable selection. Cancer Informatics.

See Also

See Also Tran

Examples

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data(NCI_60)
X <- NCI_60$aCGH
xi <- InitXi(X)