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metid_introduction.Rmd
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metid_introduction.Rmd
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---
title: "Brief introduction of metid"
author:
- name: Xiaotao Shen PhD (https://www.shen-lab.org/)
date: "Created on 2020-03-28 and updated on `r Sys.Date()`"
output:
html_document:
df_print: paged
toc: no
pdf_document:
toc: no
vignette: >
%\VignetteIndexEntry{metid}
%\VignettePackage{metid}
% \VignetteEngine{knitr::rmarkdown}
% \usepackage[utf8]{inputenc}
%\VignetteEncoding{UTF-8}
---
```{r, include=FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
out.width = "100%"
)
```
***
## **Introduction & Installation**
******************************************
*metid* is a R package which can be used for in-house (MS2) database construction, and metabolite identification based on in-house and public MS1/MS2 database.
<img src="../man/figures/Figure_1.png" align="middle" alt="" width = "100%"/>
Please install it via [github](https://github.com/tidymass/metid).
```{r,eval=FALSE,warning=FALSE, R.options=""}
if(!require(devtools)){
install.packages("devtools")
}
devtools::install_github("tidymass/metid")
```
All the demo data for `metid` are from `demoData`, so please install it first.
```{r,eval=FALSE,warning=FALSE, R.options=""}
devtools::install_github("jaspershen/demoData")
```
`metid` is a part of `tidymass`, so you can also install it by installing [`tidymass`](https://tidymass.github.io/tidymass/index.html).
## **Database construction**
******************************************
Please refer to this article: [Construct in-house MS2 datbase using metid](https://tidymass.github.io/metid/articles/database_construction.html) for database construction.
## **Public databases**
We have provide some public databases and our in-house databases, so if you want to use them, please refer this article, [Database provided for `metid`](https://tidymass.github.io/metid/articles/public_databases.html).
## **Metabolite identification**
If you want to identify metabolite without MS2 spectra, please refer to this article, [Annotate metabolites according to MS1 database using metid](https://tidymass.github.io/metid/articles/metabolite_annotation_using_MS1.html).
---
If you want to identify metabolite with MS2 spectra, please refer to this article, [Annotate metabolites according to MS2 database using metid](https://tidymass.github.io/metid/articles/metabolite_annotation_using_MS2.html).
---
If you want to identify a peak table with multiple databases, please refer to this article, [Identify peak tables with multiple databases](https://tidymass.github.io/metid/articles/multiple_databases.html).
---
If you just want to identify single peak, please refer to this article: [Identify single peak with metid](https://tidymass.github.io/metid/articles/identify_single_peak.html).
## **Other tools**
`metid` package also has some useful tools, please refer to this article, [Other tools in metid](https://tidymass.github.io/metid/articles/other_tools.html)