networkBMA (version 1.14.0)

contabs.prelim: Preliminary calculation for network assessment.

Description

Computes the quantities to be used for assessment from a proposed and a set of reference edges. For cases where there is incomplete information about the true underlying network.

Usage

contabs.prelim(network, reference, known = NULL)

Arguments

network

A network represented as a data frame in which each row corresponds to a directed edge (regulator-gene pair) with nonzero estimated probability. The first column gives the name of the regulator, the second column gives the name of the regulated gene, and the third column gives the estimated probability for the regulator-gene pair. If the third column is omitted it is assumed that all edges are assigned probability 1.

reference

A reference network represented as a two-column data frame in which each row corresponds to a regulator-gene pair (or network edge), and the columns give the corresponding regulator and target gene names, respectively. This reference network is used as the standard for determining contingency table entries.

known

A 2-column matrix of regulatory relationships that were known (hard-coded) in the modeling process that produced network. Each row corresponds to a known regulator-gene pair (edge in the network), and the columns give the corresponding regulator and target gene names, respectively. These known regulatory relationships should all be included in network (this is checked), and they may also have regulator-gene pairs in common with reference.

Value

A list with the following components:

network

A network represented as a data frame in which each row corresponds to an edge with nonzero estimated probability. This is the input network with edges from the known regulatory relationships and edges outside of the domain defined by the output version of reference removed.

reference

A reference network represented as a two-column data frame in which each row corresponds to an edge, and the columns give the regulator and target genes, respectively. This is the input reference reduced by the known regulatory relationships.

size

The size of the network formed by pairs (r,g) in which r is any regulator g is any gene from the output version of reference, reduced by any known regulatory relationships.

Details

This function accomplishes the preprocessing step from contabs.newtBMA to produce the appropriate input to contabs to produce contingency tables.

See Also

networkBMA,contabs.netwBMA,contabs

Examples

## Not run: 
# data(vignette)
# 
# dim(timeSeries)
# colnames(timeSeries)
# table(timeSeries$replicate)
# table(timeSeries$time)
# 
# dim(reg.known)
# colnames(reg.known)
# 
# dim(reg.prob)
# 
# edges <- networkBMA(data = timeSeries[,-(1:2)],
#                     nTimePoints = length(unique(timeSeries$time)),
#                     prior.prob = reg.prob, known = reg.known)
# 
# prelim <- contabs.prelim( network = edges, reference = referenceNetwork, 
#                        known = reg.known)
# contabs( network = prelim$network, reference = prelim$reference,
#          size = prelim$size, thresholds = prelim$thresholds)
# 
# contabs.netwBMA( network = edges, reference = referenceNetwork, 
#                  known = reg.known)
# ## End(Not run)