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https://github.com/ethanbass/mzinspectr
Load and analyze MS-DIAL alignment files in R for analysis of mass spectrometry data.
https://github.com/ethanbass/mzinspectr
cheminformatics gc-ms lc-ms metabolomics r r-package r-stats
Last synced: 4 days ago
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Load and analyze MS-DIAL alignment files in R for analysis of mass spectrometry data.
- Host: GitHub
- URL: https://github.com/ethanbass/mzinspectr
- Owner: ethanbass
- License: gpl-3.0
- Created: 2022-10-22T21:52:37.000Z (about 2 years ago)
- Default Branch: master
- Last Pushed: 2024-11-05T17:17:43.000Z (about 2 months ago)
- Last Synced: 2024-11-05T18:28:26.861Z (about 2 months ago)
- Topics: cheminformatics, gc-ms, lc-ms, metabolomics, r, r-package, r-stats
- Language: R
- Homepage:
- Size: 180 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE.md
Awesome Lists containing this project
README
# mzinspectr
[](https://ethanbass.r-universe.dev)
[](https://doi.org/10.5281/zenodo.10426253)
[](https://github.com/emersion/stability-badges#experimental)
A few functions for analyzing mass spectrometry alignments in R. Currently, MS-DIAL `.txt` alignment files are supported.
### Installation
It's recommended to install mzinspectr directly from GitHub.
```
install.packages("remotes")
remotes::install_github("https://github.com/ethanbass/mzinspectr/")
```
It can also be installed via [R Universe](https://ethanbass.r-universe.dev/):
```
install.packages("mzinspectr", repos="https://ethanbass.r-universe.dev/", type="source")
```
### Exporting alignments from MS-DIAL.
Export your alignment from MS-DIAL by selecting the `Export:Alignment Result` menu. Select Area or Height as appropriate.
### Reading alignment into R
Read your alignment into R using the `ms_read_alignment` function, providing the path to your MS-DIAL alignment file. This will produce a list of matrices. The first element will be the actual peak table (`tab`) with the areas or heights of the features detected by MS-DIAL. The second element will contain the peak metadata returned by MS-DIAL such as retention indices, mass spectra, and any identifications done in MS-DIAL (`peak_meta`). The third element is intended to hold sample metadata (`sample_meta`) provided by the user, which can be added using the `ms_attach_metadata` function.
The `ms_attach_metadata` function takes three arguments: an MS-DIAL alignment object (`x`), a dataframe or matrix containing the sample metadata (`meta`), and a string specifying the column in `meta` to be matched with the names of the samples (`col`).
### Normalization
There are currently several different options for feature normalization, including normalization by an internal standard (`ms_normalize_itsd`), total sum normalization (`ms_normalize_tsn`) and probabilistic quotient normalization (`ms_normalize_pqn`). You can also subtract the mean or median value from a set of blanks from each peak using the `ms_subtract_blanks` function.
### Peak identification
There is preliminary support for peak identification by searching a user-provided mass-spectral database through the `ms_search_spectra` function. The database can be loaded into R from an MSP file using the It takes several parameters, including an ms-dial alignment object (`x`), a spectral database (`db`), the column or columns to identify (`cols`), the maximum retention index shift to exclude a match from consideration (`ri_thresh`), the relative weight to give spectral similarity versus retention index similarity (`spectral_weight`), the number of results to return (`n_results`), and the number of cores to use for parallel processing (`mc.cores`).
To compile a mass spectral database, I recommend using [mspcompiler](https://github.com/QizhiSu/mspcompiler).
### Visualization
Spectra can be plotted using either "base R" graphics or "plotly" graphics using the `ms_plot_spectrum` function, which takes an ms-dial alignment object (`x`) and a column index (`col`) as argument.
### Citation
If you use mzinspectr in published work, please cite it as follows:
Bass, E. (2023). mzinspectr: Read and Analyze Mass Spectrometry Alignment Files (version 0.4.2). https://doi.org/10.5281/zenodo.10426253.