s4vdp4-package: Performance enhancements and SciDB array support for the s4vd...

In Paradigm4/s4vdp4: Performance enhancements and SciDB matrix support for the s4vd biclustering package.

Description

Performance enhancements and SciDB array for the s4vd package. We also fix a bug in the ssvdBC function.

Details

Package:	ssvd_p4
Type:	Package
Version:	1.0
Date:	2012-04-05
License:	What license is it under?

We replace the 'ssvd' and 'ssvdBC' functions in the s4vd package. Performance enhancements include using the IRLB method to compute required partial singular value decompositions, and a mathematically equivalent, but computationally more efficient, reformulation of the BIC optimization routine. See the package vignette for a detailed summary of the changes.

Author(s)

B. W. Lewis <[e-mail]>

References

Biclustering via Sparse Singular Value Decomposition, M. Lee, H. Shen, J. Huang, J. S. Marron, Biometrics 66, pp. 1087-1095, December 2010. http://cran.r-project.org/web/packages/s4vd/index.html

Examples

## Not run: 
library("s4vd")
# Lung is a small data set included in the biclust package.
data(lung)
A = lung
cat("Starting standard s4vd\n")
t1 = proc.time()
x = biclust(A, method=BCssvd, K=1)
print(proc.time()-t1)

library("s4vdp4")
scidbconnect()

cat("Starting P4 s4vd\n")
scidbremove("A",error=invisible)
X = as.scidb(A)
t1 = proc.time()
x1 = biclust(X, method=BCssvd, K=1)
print(proc.time()-t1)

## End(Not run)

Paradigm4/s4vdp4 documentation built on May 8, 2019, 12:55 a.m.