Published May 29, 2023
| Version v0.5.7
Software
Open
TwoSampleMR R package
Description
- Move car package to Suggests to allow TwoSampleMR to install on R between versions 4.0.0 and 4.1.0
- In DESCRIPTION use pkgdepends syntax for MRPRESSO package due its repository name being different to the package name so that installing TwoSampleMR under pak continues to work
- Various minor code tweaks to fix 2 R CMD check notes
- Add Cairo package to Suggests list (thanks @hdraisma)
- Fix error in outcome data vignette (thanks @hdraisma)
- Some p-values that should have been ~0 were being stored as 1 in the elasticsearch database. This has now been fixed and those datasets have been clumped again to re-define the tophits. A full list of affected GWAS is available here: https://github.com/MRCIEU/opengwas-infpval-fix
- Updated steiger filtering to use effective sample size for case control studies (thanks to @niekverw)
- Fixed issue with tri-allelic SNPs in harmonisation. Credit to Clare Horscroft (@chorscroft) for spotting the error and fixing
- Fixed an issue with experimental version of local multivariable MR method. Credit to Mischa Lundberg (@MischaLundberg).
- Catching edge cases for retrieving sample size meta data
- Updating default rsq estimation function to use beta and standard error instead of p-value, should improve numerical stability
- Allow chr and pos to be read in from local summary data files
- When reading in local data without p-values, editing the inferred p-value method to be two-sided
- All images in the vignettes (and hence also in the rendered pkgdown website) now have accompanying alt text descriptions
- The accompanying website for the package now uses Bootstrap 5, which means a search facility is enabled
- The NAMESPACE has been simplified, hence the package load time is very slightly improved
Notes
Please cite this software using the metadata from 'preferred-citation'.
Files
MRCIEU/TwoSampleMR-v0.5.7.zip
Files
(3.0 MB)
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md5:ebd941896f03f7ead07384c507325064
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Additional details
Related works
- Is supplement to
- https://github.com/MRCIEU/TwoSampleMR/tree/v0.5.7 (URL)