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https://github.com/jware-solutions/ggca
Blazing fast Gene/GEM Correlation Analysis for Rust and Python
https://github.com/jware-solutions/ggca
bioinformatic correlation correlation-analysis gene-expression gene-expression-modulation python rust
Last synced: about 1 month ago
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Blazing fast Gene/GEM Correlation Analysis for Rust and Python
- Host: GitHub
- URL: https://github.com/jware-solutions/ggca
- Owner: jware-solutions
- License: gpl-3.0
- Created: 2020-12-09T00:25:33.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-07-09T19:43:24.000Z (2 months ago)
- Last Synced: 2024-07-09T21:14:07.489Z (2 months ago)
- Topics: bioinformatic, correlation, correlation-analysis, gene-expression, gene-expression-modulation, python, rust
- Language: Rust
- Homepage: https://crates.io/crates/ggca
- Size: 11.6 MB
- Stars: 4
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-blazingly-fast - ggca - Blazing fast Gene/GEM Correlation Analysis for Rust and Python (Rust)
README
# Gene GEM Correlation Analysis (GGCA)
[](https://github.com/jware-solutions/ggca/actions/workflows/ci.yml)
Computes efficiently the correlation (Pearson, Spearman or Kendall) and the p-value (two-sided) between all the pairs from two datasets. It also supports [CpG Site IDs][cpg-site].
**IMPORTANT**: GGCA is the heart of a platform called Multiomix. On the official website you will be able to use this library in a fast and agile way through a friendly graphical interface (along with many extra features!). Go to https://multiomix.org/ to get started now!
[Python PyPi][pypi-site] | [Rust Crate][crate-site]
## Index
- [Requirements](#requirements)
- [Usage](#usage)
- [Python](#python)
- [Rust](#rust)
- [Contributing](#contributing)
- [Considerations](#considerations)
## Requirements
You need to install [GSL][gsl] >= 2.6 in your system to use this library.
## Usage
There are a few examples in `examples` folder for both languages.
### Python
1. Install: `pip install ggca`
1. Configure and call the `correlate` method:
```python
import ggca
# Possible Correlation methods
SPEARMAN = 1
KENDALL = 2
PEARSON = 3
# Possible P-values adjustment methods
BENJAMINI_HOCHBERG = 1
BENJAMINI_YEKUTIELI = 2
BONFERRONI = 3
mrna_file_path = "mrna.csv"
gem_file_path = "mirna.csv"
try:
(result_combinations, evaluated_combinations) = ggca.correlate(
mrna_file_path,
gem_file_path,
correlation_method=PEARSON,
correlation_threshold=0.5,
sort_buf_size=2_000_000,
adjustment_method=BENJAMINI_HOCHBERG,
all_vs_all=True,
gem_contains_cpg=False,
collect_gem_dataset=None,
keep_top_n=2 # Keeps only top 2 elements
)
print(f'Number of resulting combinations: {len(result_combinations)} of {evaluated_combinations} evaluated combinations')
for combination in result_combinations:
print(
combination.gene,
combination.gem,
combination.correlation,
combination.p_value,
combination.adjusted_p_value
)
except ggca.GGCADiffSamplesLength as ex:
print('Raised GGCADiffSamplesLength:', ex)
except ggca.GGCADiffSamples as ex:
print('Raised GGCADiffSamples:', ex)
except ggca.InvalidCorrelationMethod as ex:
print('Raised InvalidCorrelationMethod:', ex)
except ggca.InvalidAdjustmentMethod as ex:
print('Raised InvalidAdjustmentMethod:', ex)
except ggca.GGCAError as ex:
print('Raised GGCAError:', ex)
```
### Rust
1. Add crate to `Cargo.toml`: `ggca = { version = "0.4.1", default-features = false }`
1. Create an analysis and run it:
```rust
use ggca::adjustment::AdjustmentMethod;
use ggca::analysis::Analysis;
use ggca::correlation::CorrelationMethod;
// File's paths
let df1_path = "mrna.csv";
let df2_path = "mirna.csv";
// Some parameters
let gem_contains_cpg = false;
let is_all_vs_all = true;
let keep_top_n = Some(10); // Keeps the top 10 of correlation (sorting by abs values)
let collect_gem_dataset = None; // Better performance. Keep small GEM files in memory
let analysis = Analysis::new_from_files(df1_path.to_string(), df2_path.to_string(), false);
let (result, number_of_elements_evaluated) = analysis.compute(
CorrelationMethod::Pearson,
0.7,
2_000_000,
AdjustmentMethod::BenjaminiHochberg,
is_all_vs_all,
collect_gem_dataset,
keep_top_n,
)?;
println!("Number of elements -> {} of {} combinations evaluated", result.len(), number_of_elements_evaluated);
for cor_p_value in result.iter() {
println!("{}", cor_p_value);
}
```
Note that [env_logger][env-logger] crate is used to provide some warning in case some mRNA/GEM combinations produce NaN values (for instance, because the input array has 0 std). In that case, you can add RUST_LOG=warn to your command to produce warnings in the stderr. E.g:
`RUST_LOG=warn cargo test --no-default-features --tests`
or
`RUST_LOG=warn cargo run --example basic --no-default-features`
## Contributing
All kind of help is welcome! Feel free o submit an issue or a PR. There are some TODOs which are listed below:
- [ ] Parallelize iterators to improve performance
- [ ] Make Rust enums accessible from Python
- [ ] Add support for Windows OS
- [X] Add Rust documentation
- [X] Add tests
- [X] Add MyPy support
### Developing
We provide a Docker image to execute all the commands listed below:
- Build for rust: cargo build [--release]
- Build for Python (uses Maturin):
1. First of all, remove the `target/wheels` folder: `rm -rf ./target/wheels`
1. Build wheels: `docker run --rm -v $(pwd):/io jwaresolutions/ggca-build:0.2.3 maturin build --release --skip-auditwheel --manylinux=2014`
1. Repair wheels to include some missing `.so` files: `docker run --rm -v $(pwd):/io jwaresolutions/ggca-build:0.2.3 ./repair-wheels.sh`
- Only for development:
- To run the examples you must run with this command due to [an issue][pyo3-issue] with Pyo3: `cargo run [--release] --no-default-features --example `
- In Python you can test with Maturin:
- Maturin develop (installs the package in your current virtualenv): `maturin develop`
- Maturin build (just builds the wheel for your current Python version): `maturin build --manylinux=1-unchecked`
- To publish in PyPi:
1. Install twine: `pip install twine`
1. Upload: `twine upload ./target/wheels/wheelhouse/*`
### Tests
All the correlation, p-values and adjusted p-values were taken from [cor.test][r-cor-test] and [p.adjust][r-p-adjust] functions from the R programming language and [statsmodels][statsmodels] package for Python language.
Data in `small_files` folder was retrieved with random sampling from the *Colorectal Adenocarcinoma (TCGA, Nature 2012)* dataset. This dataset can be downloaded from [cBioPortal datasets page][cbioportal-datasets-page] or [this direct link][colorectal-dataset].
All the correlations results were compared directly with R-Multiomics output (old version of [multiomix.org][multiomix] only available for R lang).
### Performance
We use [criterion.rs][criterion] to perform benchmarks. In case you have made a contribution you can check that no regression was added to the project. Just run `cargo bench --no-default-features` before and after your changes to perform a statistical analysis of performance.
## Considerations
If you use any part of our code, or the tool itself is useful for your research, please consider citing:
```
@article{camele2022multiomix,
title={Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation},
author={Camele, Genaro and Menazzi, Sebastian and Chanfreau, Hern{\'a}n and Marraco, Agustin and Hasperu{\'e}, Waldo and Butti, Matias D and Abba, Martin C},
journal={Bioinformatics},
volume={38},
number={3},
pages={866--868},
year={2022},
publisher={Oxford University Press}
}
```
[pypi-site]: https://pypi.org/project/ggca/
[crate-site]: https://crates.io/crates/ggca
[cpg-site]: https://en.wikipedia.org/wiki/CpG_site
[gsl]: https://www.gnu.org/software/gsl/
[pyo3-issue]: https://github.com/PyO3/pyo3/issues/1084
[r-cor-test]: https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cor.test
[r-p-adjust]: https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/p.adjust
[statsmodels]: https://www.statsmodels.org/dev/generated/statsmodels.stats.multitest.multipletests.html
[cbioportal-datasets-page]: https://www.cbioportal.org/datasets
[colorectal-dataset]: https://cbioportal-datahub.s3.amazonaws.com/coadread_tcga_pub.tar.gz
[multiomix]: https://www.multiomix.org
[env-logger]: https://docs.rs/env_logger/latest/env_logger/
[criterion]: https://github.com/bheisler/criterion.rs