trigger-net: Network-Trigger analysis

In StoreyLab/trigger-devel: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

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

  	## S4 method for signature 'trigger'
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.

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.

Value

A matrix of genome-wide regulatory probabilities with putative regulators in rows and regulated genes in columns. Note that the matrix is not symmetric. If gene i is estimated to be causal for gene j with high probability, the reverse is not true.

Author(s)

Lin S. Chen [e-mail], Dipen P. Sangurdekar [e-mail] and John D. Storey [e-mail]

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)

StoreyLab/trigger-devel documentation built on May 9, 2019, 3:11 p.m.