timesaveR

My daily work mostly entails running the same data cleaning, pre- and post-processing functions over and over again. For weeks, and weeks. Months. Years.

This rough R package includes a collections of functions doing the completely different things, their only common denominator is that they save me time.

Installation

devtools::install_github("alesssia/timesaveR")

Dependencies

• R: https://www.r-project.org/
• devtools: https://github.com/r-lib/devtools
• Functions calculating linkage disequilibrium statistics query the LDproxy Programmatic Access via API. This requires a LDlink personal token, that can be requested here.

License

timesaveR is licensed under GNU GPL v3.

Acknowledgements

While some of the functions have been developed 100% by me, others are liberal (or not so liberal) adaptations of other people's work, several of whom I had lost track. I am happy to include attribution whenever I can: if you spot your or someone else's work, please let me know.

Changelog

0.0.1.6 / 2023-12-21

Enhancements:

• Added a second function (LDtrait) that queries the GWAS Catalog this time via the LDproxy Programmatic Access
• LDproxy returns also the queried SNP (rsID)
• All functions based on the LDproxy Programmatic Access are now suppressing messages written to stderr.

0.0.1.5 / 2023-08-04

Enhancements:

• Improved inverse.normal
• Improved handling of errors/warning in LDproxy
• estimate.heritability now checks the confidence intervals when extracting the best model

0.0.1.4 / 2020-09-02

Enhancements:

• Improved handling of errors when linkage disequilibrium statistics are used
• biomart.SNP.position can now return also the variant alleles
• Added a function (biomart.SNP.rsID) that returns the rsID given the chromosomal coordinates and the alleles

0.0.1.3 / 2020-02-05

Enhancements:

• Functions biomart.SNPid.in.window can now return also the variant alleles

0.0.1.2 / 2019-10-25

Enhancements:

• Functions biomart.*.in.window can now return also the chromosomal coordinates
• Added a function (biomart.SNP.position) that returns the chromosomal coordinates of a given SNP
• Added functions to query the GWAS Catalog (GWAS.catalog.SNP and GWAS.catalog.SNP.proxy)