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0_data_import.Rmd
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0_data_import.Rmd
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---
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")
```