0_data_import.Rmd

---
author:
  - name: "Nathalia Graf Grachet"
    url: https://github.com/nathaliagg/oak_metabolomics
    affiliation: University of Arizona
editor_options: 
  chunk_output_type: console
---


## Oak Metabolic Profiling


### Libraries


Make sure `xcms` is installed.


```{r}
library(xcms)
doParallel::registerDoParallel(18)
```


### 1 - Import data

**Important** Data was already in centroid mode.


```{r}
# define metadata, ie, phenotypic data
pd <- read.csv("metadata.csv")

# get filenames from directory
files <- as.vector(paste0("/groups/tfaily/nathaliagg/uren_oak_metabolomics/data_mzxml/", pd$FileName))

# Read the data:
data_cent <- readMSData(files, 
                        pdata = new("NAnnotatedDataFrame", pd), 
                        mode = "onDisk",
                        verbose = TRUE)
```


The MS experiment is now represented as an `OnDiskMSnExp` object. 

Information stored in the `OnDiskMSnExp` object after import:
```{r}
show(data_cent)
```


## 2 - Save R object as `.RData`

Save as an R object so later, you don't need to re-import the data
```{r}
## Save data object as rds
save(data_cent, pd, file = "data_centroided.RData")
```