an object of S4 class BetaMixture, which models the densities of
first-order similarities between genes (see BetaMixture).
type
a character value giving the type of edge weights: signal-to-noise ratio
('SNR'), posterior probability ratio ('PPR') or posterior probability ('PP')
log
a logical value specifying whether or not to compute logrithms for edge weights.
sign
a logical value specifying whether a signed graph should be inferred. It is only
used when type='SNR'.
cutoff
a numeric value giving the threshold to tell the significance of an edge.
filter
a logical value specifying whether or not to filter out genes without any
significant association with all the other genes.
Details
This function first initiates an object of class PAN with
bm, which is an object of class BetaMixture that is supposed
to have been fitted.
The function infer is then invoked to infer a posterior
association network given the inputted arguments type, log,
sign, cutoff and filter.
Value
an object of class PAN with the inferred posterior
association network stored at slot graph
Mulder KW, Wang X, Escriu C, et al. (2012). Diverse epigenetic strategies
interact to control epidermal differentiation. Nature Cell Biology.
doi:10.1038/ncb2520.
Wang X, Castro MA, Mulder KW and Markowetz F (2012), Posterior association
networks and enriched functional gene modules inferred from rich phenotypic
perturbation screens, PLoS Computational Biology, doi:10.1371/journal.pcbi.1002566.