bootstrapProconaNetwork: bootstrapProconaNetwork

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

Description

This function returns a peptide co-expression network object based on a bootstrapped correlation matrix.

Usage

bootstrapProconaNetwork(networkName = "bootstrap procona", pepdat = NULL, 
    pow = NULL, powMax = 20, networkType = "signed", scaleFreeThreshold = 0.8, 
    deepSplit = 2, minModuleSize = 30, mergeThreshold = 0.1, 
    clusterType = "average", pamRespectsDendro = T, performTOPermtest = TRUE, 
    toPermTestPermutes = 100, bootstrapThreshold = 1e-04)

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	Whether the sign is considered in constructing adjacency and TOM
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.
bootstrapThreshold	When to stop resampling...

Value

returns the procona network object

Author(s)

David L Gibbs

Examples

data(ProCoNA_Data)
net <- bootstrapProconaNetwork("peptide network", peptideData,
performTOPermtest=FALSE, bootstrapThreshold=0.1)

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