buildProconaNetwork {ProCoNA} | R Documentation

## buildProconaNetwork

### Description

This function returns a peptide co-expression network object.

### Usage

    buildProconaNetwork(networkName = "ProCoNA", pepdat, pow=1,
        powMax = 20, networkType = "signed", pearson = FALSE, scaleFreeThreshold = 0.8,
        deepSplit = 2, minModuleSize = 30, mergeThreshold = 0.1,
        clusterType = "average", pamRespectsDendro = TRUE, performTOPermtest = TRUE,
        toPermTestPermutes = 100)

### Arguments

`networkName` | Name of this network
`pepdat` | This variable is the data set with rows as samples and cols as peptides
`pow` | The scaling power, NULL if unknown
`powMax` | The maximum power to be searched.
`networkType` | Should the sign be considered in constructing adjacency and TOM ("signed" or "unsigned")
`pearson` | use Pearson's cor or the robust bi-weight correlation
`scaleFreeThreshold` | The threshold for fitting to scale-free topology.. will use closest power.
`deepSplit` | Course grain control of module size
`minModuleSize` | The minimum module size allowed
`mergeThreshold` | Below this threshold, modules are merged.
`clusterType` | Clustering option
`pamRespectsDendro` | When cutting the dendrogram, pay attention to branch membership.
`performTOPermtest` | Performs permutation testing on modules
`toPermTestPermutes` | Number of permutations to do.

### Details

The procona network object contains a number of slots which store information relevant to the construction of the network. Accessor functions provide direct access to the slots. See getSlots("proconaNet") for a complete list.

### Value

returns the procona network object

### Author(s)

David L Gibbs

### Examples

    data(ProCoNA_Data)
    net <- buildProconaNetwork("peptide network", peptideData)

[Package ProCoNA version 1.18.0 Index]