splineNetRecon {splineTimeR} | R Documentation

## Network reconstruction based on partial correlation method with shrinkage approach

### Description

`splineNetRecon` reconstructs gene association networks from time-course 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.

### Usage

    splineNetRecon(eSetObject, treatmentType, probesForNR="all",
                cutoff.ggm=0.8, method="dynamic", saveEdges=FALSE)

### Arguments

`eSetObject` | `ExpressionSet` object of class `ExpressionSet` containing log-ratios or log-values of expression for a series of microarrays
`treatmentType` | a character string containing a type of `Treatment` defining samples considered for network reconstruction
`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 `"static"` and `"dynamic"` (default) - both are shrinkage methods
`saveEdges` | if `TRUE`, .Rdata file with all edges is created; default is `FALSE`

### Details

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.

### Value

An object or list of objects of class `igraph`.

If `saveEdges` is `TRUE`, .Rdata file with all possible edges is created.

### Author(s)

Agata Michna

### See Also

http://strimmerlab.org/software/genenet/

http://strimmerlab.org/software/longitudinal/

### Examples

    ## load "eSetObject" containing simulated time-course data
    data(TCsimData)

    ## define function parameters
    treatmentType = "T2"
    probesForNR = "all"
    cutoff.ggm = 0.8
    method = "dynamic"

    ## reconstruct gene association network from time-course data
    igr <- splineNetRecon(eSetObject = TCsimData, treatmentType, probesForNR, cutoff.ggm, method)
    plot(igr, vertex.label = NA, vertex.size = 3)

[Package splineTimeR version 1.15.1 Index]