getmoduleHub {DDPNA}R Documentation

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)

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.

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

Author(s)

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")
}

[Package DDPNA version 0.3.1 Index]