buildProconaNetwork: buildProconaNetwork

Description Usage Arguments Details Value Author(s) Examples

View source: R/buildNetwork.R

Description

This function returns a peptide co-expression network object.

Usage

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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

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

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