DDPNA (version 0.4.1)

getmoduleHub: getmoduleHub

Description

extract PMFG information and get Module hub proteins.

Usage

getmoduleHub(data, module, mod_num, coln = "new.ID",
             cor.sig = 0.05, cor.r = 0, cor.adj="none",
             adjustp = TRUE, hub.p = 0.05)

Value

a list contains PMFG network information. list(hub = hubgene, degreeStat = Stat, graph = g, PMFG = gg)

hub

hub information.

degreeStat

degree statistics information

graph

the original graph data frame

PMFG

PMFG graph data frame

Arguments

data

proteomic quantification data.

module

module information which is getted in Module_inf function.

mod_num

the module name which module will be calculate.

coln

column name of module contains protein IDs. it could be matched with "classifiedID"

cor.sig

a numberic value indicated that correlation p value less than cor.sig will be picked.

cor.r

a numberic value indicated that correlation r value larger than cor.r will be picked.

cor.adj

P value correction method. method information can see in p.adjust.method

adjustp

a logical value indicating whether pick hub protein by FDR methods.

hub.p

a numberic value indicated that hub proteins are p value less than hub.p.

Author

Kefu Liu

Examples

data(net)
data(imputedData)
data <- imputedData
logD <- data$log2_value
rownames(logD) <- data$inf$ori.ID
group <- gsub("[0-9]+","", colnames(logD))
Module <- Module_inf(net, data$inf)
Mod10 <- getmoduleHub(logD, Module, 10, coln = "ori.ID", adjustp = FALSE)
if (requireNamespace("MEGENA", quietly = TRUE)) {
 library(MEGENA)
 plot_subgraph(module = Mod10$degreeStat$gene,
              hub = Mod10$hub,PFN = Mod10$PMFG,
              node.default.color = "black",
              gene.set = NULL,color.code = c("grey"),show.legend = TRUE,
              label.hubs.only = TRUE,hubLabel.col = "red",hubLabel.sizeProp = 0.5,
              show.topn.hubs = 10,node.sizeProp = 13,label.sizeProp = 13,
              label.scaleFactor = 10,layout = "kamada.kawai")
}