BCSub: A Bayesian Semiparametric Factor Analysis Model for Subtype Identification (Clustering)

Gene expression profiles are commonly utilized to infer disease subtypes and many clustering methods can be adopted for this task. However, existing clustering methods may not perform well when genes are highly correlated and many uninformative genes are included for clustering. To deal with these challenges, we develop a novel clustering method in the Bayesian setting. This method, called BCSub, adopts an innovative semiparametric Bayesian factor analysis model to reduce the dimension of the data to a few factor scores for clustering. Specifically, the factor scores are assumed to follow the Dirichlet process mixture model in order to induce clustering.

Author
Jiehuan Sun [aut, cre], Joshua L. Warren [aut], and Hongyu Zhao [aut]
Date of publication
2016-10-29 10:48:09
Maintainer
Jiehuan Sun <jiehuan.sun@yale.edu>
License
GPL-2
Version
0.2

View on CRAN

Man pages

BCSub
A Bayesian semiparametric factor analysis model for subtype...
calSim
Function to calculate the similarity matrix based on the...
dmvnrm_arma
Internal function to calculate the density of multivariate...
mvrnormArma
Internal function to sample from multivariate normal...
myfind
Internal function to find matched index.
polyurncpp
Internal function to sample cluster membership indicator
samEta
Internal function to sample eta
samLamV3Cpp
Internal function to sample Lambda
samMu
Internal function to sample cluster-specific means of eta
samRho2
Internal function to sample rho
samSig
Internal function to sample gene-specific variances
samSige
Internal function to sample variances for eta

Files in this package

BCSub
BCSub/src
BCSub/src/Makevars
BCSub/src/factor_DP_fun.cpp
BCSub/src/Makevars.win
BCSub/src/RcppExports.cpp
BCSub/NAMESPACE
BCSub/R
BCSub/R/RcppExports.R
BCSub/R/factor_DP_fun.R
BCSub/MD5
BCSub/DESCRIPTION
BCSub/man
BCSub/man/samSige.Rd
BCSub/man/BCSub.Rd
BCSub/man/polyurncpp.Rd
BCSub/man/samLamV3Cpp.Rd
BCSub/man/samRho2.Rd
BCSub/man/samEta.Rd
BCSub/man/myfind.Rd
BCSub/man/mvrnormArma.Rd
BCSub/man/calSim.Rd
BCSub/man/samSig.Rd
BCSub/man/dmvnrm_arma.Rd
BCSub/man/samMu.Rd