In tidymass/tinytools: All the usefull tools for MS data processing and analysis

knitr::opts_chunk$set(echo = TRUE)

**Analysis report**

Laboratory for Mass Spectrometry and Metabolomics ([ZHU LAB](http://www.zhulab.cn/))

IRCBC, Chinese Academy of Sciences, Shanghai, China.

`r format(Sys.Date())`

---

INTRODUCTION

**MetDNA (version 1.1)**: Created in 2018 by Xiaotao Shen, Xin Xiong and Ruohong Wang from Dr. Zheng-Jiang Zhu lab, Chinese Academy of Sciences.

---

PARAMETERS

Table 1: Parameter setting

library(knitr)
load("parameter")
kable(parameter, format = "markdown")

---

SAMPLE INFORMATION

Figure 1: Peak intensity profile for positive mode (left panel) and negative mode (right panel).

---

METABOLITE IDENTIFICATION

Figure 2: The number of identified metabolites (left panel) and peak and metabolite redundancy (right panel). (Positive mode)

Figure 3: The number of identified metabolites (left panel) and peak and metabolite redundancy (right panel). (Negative mode)

Figure 4: The confidence levles of identified metabolites. (Positive mode)

Figure 5: The confidence levles of identified metabolites. (Negative mode)

---

PATHWAY ENRICHMENT ANALYSIS

Figure 6: Volcano plot (left panel) and summary of enriched pathways (right panel).

Table 2: The detailed information of enriched pathways.

library(knitr)
if(any(dir() == "msea")){
load("msea")  
msea.result <- msea@msea
pathway.name.id <- rownames(msea.result)
pathway.name <- unlist(lapply(strsplit(pathway.name.id, split = ";"), function(x) x[1]))
pathway.id <- unlist(lapply(strsplit(pathway.name.id, split = ";"), function(x) x[2]))
pathway.id <- paste("[", pathway.id, "]", "(http://www.kegg.jp/kegg-bin/show_pathway?", pathway.id, ")", sep = "")
msea.result$Overlap <- msea.result$Overlap*100/msea.result$Pathway.length
rownames(msea.result) <- NULL
msea.result <- msea.result[,-2]
msea.result <- data.frame(pathway.name, pathway.id, msea.result, stringsAsFactors = FALSE)

colnames(msea.result) <- c("Pathway name", "Pathway ID", "P value",
                              "P value (FDR adjust)", "Pathway size", "Overlap (%)")

temp.idx <- which(msea.result[,3] < 0.05)
if(length(temp.idx) > 0){
  msea.result <- msea.result[temp.idx,]
}
kable(msea.result)
}

tidymass/tinytools documentation built on Jan. 2, 2022, 5:18 p.m.