bootstrapProconaNetwork: bootstrapProconaNetwork

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

Examples

Run this code


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

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