trigger (version 1.18.0)

trigger.net-methods: Network-Trigger analysis

Description

Network-Trigger analysis estimates the joint posterior probability of causal regulation for each pair of genes in the genome. These probabilities can further be used to construct a gene regulatory network.

Usage

"trigger.net"(triggerobj, gender = NULL, idx = NULL, 
	Bsec = 100, prob.cut = 0.7, include.loc = TRUE, seed = 123, inputfile = NULL)

Arguments

triggerobj

An object of class trigger containing slot loc.obj with local-linkage probabilities and marker indices of the best local-linkage markers for genes in the genome. See trigger and trigger.loclink for details.

gender

Optional. When computing statistics involving markers on sex chromosome, gender of each sample should be specified.

idx

Optional. One can specify the indices of selected genes as putative regulators. By default, all the genes will be selected as putative regulators.

Bsec

Number of iterations to perform when estimating null statistics for secondary-linkage and conditional independence.

prob.cut

Probability threshold. The joint regulatory probabilities of a regulator to all the other genes will be set to zero if the local-linkage probability of the regulator is below the threshold; default prob.cut = 0.7.

include.loc

Logical. If TRUE, the estimated posterior probability of regulation is more conservative.

seed

Optional. A numeric seed for reproducible results.

inputfile

Optional. If provided, reads in the probability matrix from working directory.

Value

Details

The option idx contains the indices of putative regulator genes. When the data set is large, one can use this option by selecting a subset of genes as putative regulators in one computation and parallel-computes the genome-wide regulatory probability. If idx=NULL, all the genes will be computed for probability of regulation to other genes in the data.

If include.loc = TRUE, the joint posterior probability of regulation is the product of local-linkage, secondary-linkage and conditional independence. Otherwise, it is the product of secondary-linkage and conditional independence. The local-linkage is not a necessary condition for calculating regulation probability. If the probability of local-linkage is considered, the joint probability of regulation is more conservative. See references for details.

References

Chen L.S., Emmert-Streib F., and Storey J.D. (2007) Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biology, 8: R219.

See Also

trigger.loclink, trigger.netPlot2ps and trigger.trait

Examples

 ## Not run: 
#   data(yeast)
#   attach(yeast)
#   triggerobj <- trigger.build(marker = marker, exp = exp, 
#             marker.pos = marker.pos, exp.pos = exp.pos)
#   triggerobj <- nettrig.loc(triggerobj, window.size = 30000)
#   trig.prob <- trigger.net(triggerobj, Bsec = 100)
#   netPlot2ps(trig.prob)
#   detach(yeast)
# ## End(Not run)