In ZhuMSLab/MetDNA: MetDNA

knitr::opts_chunk$set(echo = TRUE)

**Analysis of report**

Xiaotao Shen, Zhengjiang Zhu

`r format(Sys.Date())`

---

(1) INTRODUCTION

MetDNA is used for metabolite annotation and dysregulated network analysis of untargeted metabolomics.

---

(2) PARAMETERS

Table 1: The parameter setting of this analysis

library(knitr)
load("parameter")
colnames(parameter) <- c("Patameter", "Value", "Meaning")
kable(parameter, format = "markdown")

---

(3) SAMPLE INFORMATION

---

(4) METABOLITE ANNOTATION

The metabolite annotation is based on metabolic reaction network.

Confidence level (from grade 1 to grad 4) is assigned to each metabolie.

---

(5) Dysregulated network analysis

Dysregulated peaks (according to pvalues) are used to identify dysregulated modules. The dysregulated modules with p values less than 0.05 are combined as dysregulated network. Metabolite set analysis (MSEA) is used to annotate functions of each module. The MSEA result for each module can be found in /Dysregulated_network_analysis_result_POS/module_information/Module_MSE analysis.

Table 2: The information of dysregualted modules. The detailed information can be got from module.result.csv in /Dysregulated_network_analysis_result_POS/module_information

library(knitr)
load("module.result")
temp.idx <- which(module.result$p.value < 0.05)
if(length(temp.idx) == 0 & nrow(module.result) > 5){
  temp.idx <- 1:5
}else{
  temp.idx <- temp.idx
}

overlap <- as.numeric(module.result$`Detected metabolite number`)*100/as.numeric(module.result$`Module size`)
module.result$`Detected metabolite number` <- overlap
colnames(module.result)[5] <- "Overlap (%)"
kable(module.result[temp.idx,c(1,2,3,4,5,13)])

Table 3: The information of dysregualted networks. The detailed information can be got from dysregulated.network.MSEA.csv in /Dysregulated_network_analysis_result_POS/pathway_information.

library(knitr)
load("dn.result")
temp.idx <- which(dn.result$q.value < 0.05)
if(length(temp.idx) == 0 & nrow(module.result) > 5){
  temp.idx <- 1:5
}else{
  temp.idx <- temp.idx
}

name <- rownames(dn.result)
name <- unlist(lapply(strsplit(name, split = ";"), function(x){x[1]}))
dn.result$Overlap <- dn.result$Overlap*100/dn.result$Pathway.length
dn.result <- data.frame(name, dn.result, stringsAsFactors = FALSE)
rownames(dn.result) <- NULL
colnames(dn.result) <- c("Pathway name", "p value", "p value(adjusted)", "FDR", "Pathway size", "Overlap (%)")
kable(dn.result[temp.idx, -4])

ZhuMSLab/MetDNA documentation built on March 29, 2022, 5:45 p.m.