bootstrapProconaNetwork {ProCoNA} | R Documentation |
This function returns a peptide co-expression network object based on a bootstrapped correlation matrix.
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)
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... |
returns the procona network object
David L Gibbs
data(ProCoNA_Data) net <- bootstrapProconaNetwork("peptide network", peptideData, performTOPermtest=FALSE, bootstrapThreshold=0.1)