slfm: Tools for Fitting Sparse Latent Factor Model

Set of tools to find coherent patterns in microarray data using a Bayesian sparse latent factor model (Duarte and Mayrink 2015 - http://link.springer.com/chapter/10.1007%2F978-3-319-12454-4_15). Considerable effort has been put into making slfm fast and memory efficient, turning it an interesting alternative to simpler methods in terms of execution time. It implements versions of the SLFM using both type of mixtures: using a degenerate distribution or a very concentrated normal distribution for the spike part of the mixture. It also implements additional functions to help pre-process the data and fit the model for a large number of arrays.

Author
Joao Duarte and Vinicius Mayrink
Date of publication
2015-08-10 09:09:59
Maintainer
Joao Duarte <jdanielnd@gmail.com>
License
GPL-2
Version
0.2.2
URLs

View on CRAN

Man pages

plot_matrix
Plot matrix
process_matrix
Pre-process data for SLFM
slfm
Sparse Latent Factor Model
slfm_list
Fit SLFM to the matrices inside a directory
slfm-package
slfm: the sparse latent factor model package for R.

Files in this package

slfm
slfm/src
slfm/src/Makevars
slfm/src/slfm_MNN.cpp
slfm/src/gibbs.cpp
slfm/src/slfm_MDN.cpp
slfm/src/Makevars.win
slfm/src/RcppExports.cpp
slfm/NAMESPACE
slfm/NEWS
slfm/R
slfm/R/process_matrix.r
slfm/R/plot_matrix.r
slfm/R/class_interval.r
slfm/R/RcppExports.R
slfm/R/slfm_list.r
slfm/R/slfm.r
slfm/R/slfm-package.r
slfm/MD5
slfm/DESCRIPTION
slfm/man
slfm/man/slfm_list.Rd
slfm/man/process_matrix.Rd
slfm/man/slfm-package.Rd
slfm/man/plot_matrix.Rd
slfm/man/slfm.Rd