---
title: 'pathway analysis (mummichog)'
author: "Hemi Luan"
date: "Modified: 2019. Compiled: `r format(Sys.Date(), '%d %b %Y')`"
output: 
  BiocStyle::html_document:
    toc: true
       
vignette: >
  %\VignetteIndexEntry{statTarget2 for pathway analysis }
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}  
---

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown()
```

```{r, echo = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
```


 
# statTarget result for pathway analysis using mummichog approach.

## Pathways analysis by using MS peaks with accurate mass 


1. to get the p.value from the file in /statTarget/statAnalysis/Univariate/Pvalues
  

2. to get the fold.change from the file in /statTarget/statAnalysis/Univariate/Fold_Changes
  

3. to get the m.z from the .tsv file from the xcms output.
  

4. to use the EXCEL for generation the ".txt" format with `column named m.z, p.value and t.score (fold.change value)`
  

submit the table to MS to pathway analysis panel in metaboanalyst web: https://www.metaboanalyst.ca/MetaboAnalyst/faces/upload/PeakUploadView.xhtml