getmoduleHub: getmoduleHub

In liukf10/TEST: Disease-Drived Differential Proteins and Proteome-Wide Co-Expression Network Associated Analysis

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,
             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.
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(s)

Kefu Liu

Examples

rm(list = ls())
library(DDPNA)
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")
}

liukf10/TEST documentation built on May 20, 2019, 12:59 a.m.