stabilitySelection {RNAseqNet} | R Documentation |
stabilitySelection
implements the regularization parameter selection
of (Liu et al., 2010) called 'Stability Approach to Regularization Selection'
(StARS).
stabilitySelection(counts, lambdas = NULL, B = 20)
counts |
a n x p matrix of RNA-seq expression (numeric matrix or data frame) |
lambdas |
a sequence of decreasing positive numbers to control the
regularization (numeric vector). Default to |
B |
number of iterations for stability selection. Default to 20 |
When input lambdas
are null the default sequence of
glmnet
(see GLMnetwork
for details).
S3 object of class stabilitySelection
: a list consisting of
lambdas |
numeric regularization parameters used for regularization path |
B |
number of iterations for stability selection |
best |
index of the regularization parameter selected by StARS
in |
variabilities |
numeric vector having same length than lambdas and providing the variability value as defined by StARS along the path |
Alyssa Imbert, alyssa.imbert@gmail.com Nathalie Vialaneix, nathalie.vialaneix@inrae.fr
Liu, H., Roeber, K. and Wasserman, L. (2010) Stability approach to regularization selection (StARS) for high dimensional graphical models. In Proceedings of Neural Information Processing Systems (NIPS 2010), 23, 1432-1440, Vancouver, Canada.
data(lung)
lambdas <- 4 * 10^(seq(0, -2, length = 5))
stability_lung <- stabilitySelection(lung, lambdas = lambdas, B = 4)
## Not run: plot(stability_lung)