buildProconaNetwork: buildProconaNetwork

In ProCoNA: Protein co-expression network analysis (ProCoNA).

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)

ProCoNA documentation built on Nov. 1, 2018, 3:28 a.m.