Description Usage Arguments Details Value Examples
MCMC with bipartite graph
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whole |
Vector of character strings with names of whole nodes (gene-sets) |
part |
Vector of 0's and 1's indicating active part nodes; names are the names of the part nodes (genes) |
edge |
Matrix with two columns; each row indicates an edge between a whole node and a part node |
alpha |
Parameter alpha (0 < alpha < gamma < 1) |
gamma |
Parameter gamma (0 < alpha < gamma < 1) |
p |
Parameter p (0 < p < 1) |
nburn |
Number of burn-in generations |
ngen |
Number of sample generations |
sub |
Subsample rate for burn-in and sample files |
penalty |
Penalty per illegal node to loglikelihood |
initial |
Initial state (see Details) |
The initial
argument can take one of three values:
"inactive"
- all whole nodes inactive; "random"
- all
whole nodes active with probability p
, no illegal nodes; or
"high"
- all nodes with proportion of connected part nodes
with response equal to 1 above 0.4 are active, no illegal nodes.
data frame with "whole" results;
Name |
The names of whole nodes |
ActiveProbability |
The marginal posterior probabilities of whole nodes |
Count |
Number of active samples for each whole node |
Sample |
Number of generated samples for each whole node |
Degree |
The degree of each whole node |
Response |
The response of each whole node |
dimburn + sample detail are included as an attribute, "samples"
, which is a matrix.
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