diff --git a/HELP.md b/HELP.md new file mode 100644 index 0000000000000000000000000000000000000000..4474ad82b10b76871c7eb87224fb7b5c0183088c --- /dev/null +++ b/HELP.md @@ -0,0 +1,68 @@ +j2s: Deriving stratified effects from joint models investigating Gene-Environment Interactions +====== + +The python3 script **j2s.py** allows for the estimation of genetic effect sizes in unexposed and exposed individuals separately from joint models investigating Gene-Environment interactions when the exposure is binary. A pre-print of the publication is available [here](https://www.biorxiv.org/content/10.1101/693218v1). + +Prerequisite +------------ + +To execute the script, python3 must be installed as weel as the following Python packages: + + pandas (version 0.22.0) + + numpy (version 1.13.3) + + scipy (version 0.19.1) + +Execution +------------ + +To use the script, type the following command: + +``` bash +python3 INFILE N N_EXPOSED OUTFILE +``` + +with: + * INFILE is the path to the input file describing the summary statitics in the joint model, + * N is the total sample size, + * N_EXPO is the number of exposed (E = 1) individuals, + * OUTFILE is the path to the outputfile. + +Description of the input files +------------ + +The input file has 7 mandatory columns: + * the identifier of the variant (e.g rs number) labelled 'MarkerName' + * the main genetic effect size labelled 'Effect' + * the standard error of the main genetic effect size labelled 'StdErr' + * the interaction effect size labelled 'IntEffect' + * the standard error of the interaction effect size labelled 'IntStdErr' + * the covariance between the main genetic effect size and the interaction effect size labelled 'IntCov' + * the sample size of the variant labelled 'N' + +| MarkerName | Effect |StdErr |IntEffect |IntStdErr |IntCov |N | +| ------------ | -------- | ----------- | ----------- | ------------ | -------------| ------ | +| rs1 | 0.06464 | 0.09853 | 0.03685 | 0.1539 | -0.009603 | 302478 | +| rs2 | 0.1482 | 0.0439 | 0.1071 | 0.05265 | -0.001922 | 551772 | +| rs3 | 0.2428 | 0.06389 | 0.1027 | 0.07648 | -0.004073 | 537523 | +| rs4 | -0.1821 | 0.05173 | -0.06716 | 0.06105 | -0.002671 | 540537 | +| rs4 | -0.1665 | 0.04127 | -0.05506 | 0.0498 | -0.001692 | 527550 | + +This format corresponds to the output of the METAL software performing the joint test ([Manning et al, 2011](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312394/)) + +Short tutorial +-------------- + + +Bug report / Help +----------------- + +Please open an issue if you find a bug. + +Code of conduct +--------------- + +Please note that this project is released with a [Contributor Code of Conduct](https://gitlab.pasteur.fr/statistical-genetics/j2s/blob/master/code-of-conduct.md). By participating in this project you agree to abide by its terms. + +License +------- + +This project is licensed under the MIT License - see the [LICENSE.md](https://gitlab.pasteur.fr/statistical-genetics/j2s/blob/master/LICENSE) file for details diff --git a/code-of-conduct.md b/code-of-conduct.md new file mode 100644 index 0000000000000000000000000000000000000000..b965667f9f543d3577e683640345642f7429ba55 --- /dev/null +++ b/code-of-conduct.md @@ -0,0 +1,73 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to making participation in our project and +our community a harassment-free experience for everyone, regardless of age, body +size, disability, ethnicity, gender identity and expression, level of experience, +nationality, personal appearance, race, religion, or sexual identity and +orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or + advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic + address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces +when an individual is representing the project or its community. Examples of +representing a project or community include using an official project e-mail +address, posting via an official social media account, or acting as an appointed +representative at an online or offline event. Representation of a project may be +further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting the project team at [this adress](vlaville@pasteur.fr). All +complaints will be reviewed and investigated and will result in a response that +is deemed necessary and appropriate to the circumstances. The project team is +obligated to maintain confidentiality with regard to the reporter of an incident. +Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, +available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html + +[homepage]: https://www.contributor-covenant.org