buildProconaNetwork {ProCoNA} | R Documentation |
This function returns a peptide co-expression network object.
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)
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. |
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.
returns the procona network object
David L Gibbs
data(ProCoNA_Data) net <- buildProconaNetwork("peptide network", peptideData)