netresponse (version 1.32.2)

ICMg.combined.sampler: ICMg.combined.sampler

Description

Main function of the ICMg algorithm. ICMg.combined.sampler computes samples from the posterior of the assignments of datapoints (interactions and expression profiles) to latent components. From these we can then obtain component membership distributions and clusterings for genes.

Usage

ICMg.combined.sampler(L, X, C, alpha = 10, beta = 0.01, pm0 = 0, V0 = 1,
  V = 0.1, B.num = 8, B.size = 100, S.num = 20, S.size = 10,
  C.boost = 1)

Arguments

L

N x 2 matrix of link endpoints (N = number of links).

X

M x D matrix of gene expression profiles (M = number of nodes, D = number of observations).

C

Number of components.

alpha

Hyperparameter describing the global distribution over components, larger alpha gives a more uniform distribution.

beta

Hyperparameter describing the component-wise distributions over nodes, larger beta gives a more uniform distribution.

pm0

Hyperparameter describing the prior mean of the expression profiles, should be zero.

V0

Hyperparameter describing the variation of the component-wise expression profiles means around pm0.

V

Hyperparameter describing the variation of gene-specific expression profiles around the component-wise means.

B.num

Number of burnin rounds.*

B.size

Size of one burnin round.*

S.num

Number of sample rounds.*

S.size

Size of one sample round.*

C.boost

Set to 1 to use faster iteration with C, set to 0 to use slower R functions.

Value

• Returns samples as a list:
• z
  S.num x N matrix of samples of component assignments for links.
• w
  S.num x M matrix of samples of component assignments for gene expression profiles.
• convl
  Vector of length (B.num + S.num) with convergence estimator values for link sampling.
• convn
  Vector of length (B.num + S.num) with convergence estimator values for node sampling.
• countsl
  (B.num + S.num) x C matrix of link component sizes.
• countsn
  (B.num + S.num) x C matrix of node component sizes.
• additionally all parameters of the run are included in the list.

Details

One run consists of two parts, during burnin the sampler is expected to mix, after which the samples are taken. Information about convergence (convN and convL are estimates of convergence for link and node sampling, respectively) and component sizes are printed after each burnin/sample round. For example: B.num=8, B.size=100, S.num=20, S.size=10, runs 800 burnin iterations in 8 rounds and then takes 20 samples with an interval of 10 iterations.

References

Parkkinen, J. and Kaski, S. Searching for functional gene modules with interaction component models. BMC Systems Biology 4 (2010), 4.

See Also

ICMg.links.sampler

Examples

data(osmo) # Load data set
  res <- ICMg.combined.sampler(osmo$ppi, osmo$exp, C=10)