Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/splineNetRecon.R
splineNetRecon
reconstructs gene association networks from timecourse data. Based on given object of class ExpressionSet
, longitudinal data object is created. Subsequantly the function estimates edges using partial correlation method with shrinkage approach applying ggm.estimate.pcor
and network.test.edges
functions. As a result an object or list of object of class igraph
is created.
1 2  splineNetRecon(eSetObject, treatmentType, probesForNR="all",
cutoff.ggm=0.8, method="dynamic", saveEdges=FALSE)

eSetObject 

treatmentType 
a character string containing a type of 
probesForNR 
a vector of character string containing names/IDs used for network reconstruction 
cutoff.ggm 
number or vector of numbers between 0 and 1 defining cutoff for significant posterior probability; default value is 0.8 
method 
method used to estimate the partial correlation matrix; available options are 
saveEdges 
if 
The input eSetObject
must be provided as an object of class ExpressionSet
which contains SampleName
, Time
, Treatment
and if applicable Replicates
variables (columns) included in the phenotypic data of the eSetObject
(pData(eSetObject)
). Two types of Treatment
defining two groups to compare have to be definied.
Gene association network reconstruction is conducted for a selected type of Treatment
. This allows to find regulatory association between genes under a certain condition (treatment). First, a longitudinal
data object of the gene expression data with possible repicates is created. This object is used to estimate partial correlation with selected shrinkage method ("dynamic"
or "static"
) with the ggm.estimate.pcor
function (for details see ggm.estimate.pcor
function help). Finally, the network.test.edges
function estimates the probabilities for all possible edges and lists them in descending order (for details see network.test.edges
help).
cutoff.ggm
can be a single number or a vector of numbers. If more than one value for cutoff.ggm
is definied than function returns a list
of objects of class igraph
for each definied cutoff.ggm
value. Otherwise a single object of class igraph
with one selected probability is returned.
An object or list of objects of class igraph
.
If saveEdges
is TRUE
, .Rdata file with all possible edges is created.
Agata Michna
http://strimmerlab.org/software/genenet/
http://strimmerlab.org/software/longitudinal/
1 2 3 4 5 6 7 8 9 10 11 12  ## load "eSetObject" containing simulated timecourse data
data(TCsimData)
## define function parameters
treatmentType = "T2"
probesForNR = "all"
cutoff.ggm = 0.8
method = "dynamic"
## reconstruct gene association network from timecourse data
igr < splineNetRecon(eSetObject = TCsimData, treatmentType, probesForNR, cutoff.ggm, method)
plot(igr, vertex.label = NA, vertex.size = 3)

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