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.
devtools::install_github("alesssia/timesaveR")- 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.
timesaveR is licensed under GNU GPL v3.
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.
Enhancements:
- Added a second function (
LDtrait) that queries the GWAS Catalog this time via the LDproxy Programmatic Access LDproxyreturns also the queried SNP (rsID)- All functions based on the LDproxy Programmatic Access are now suppressing messages written to
stderr.
Enhancements:
- Improved
inverse.normal - Improved handling of errors/warning in
LDproxy estimate.heritabilitynow checks the confidence intervals when extracting the best model
Enhancements:
- Improved handling of errors when linkage disequilibrium statistics are used
biomart.SNP.positioncan now return also the variant alleles- Added a function (
biomart.SNP.rsID) that returns the rsID given the chromosomal coordinates and the alleles
Enhancements:
- Functions
biomart.SNPid.in.windowcan now return also the variant alleles
Enhancements:
- Functions
biomart.*.in.windowcan 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.SNPandGWAS.catalog.SNP.proxy)