Software Open Access
TwoSampleMR R package
Hemani, Gibran;
Haycock, Philip;
Zheng, Jie;
Gaunt, Tom;
Elsworth, Ben;
Palmer, Tom
- 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
Please cite this software using the metadata from 'preferred-citation'.
Files
(3.0 MB)
| Name | Size | |
|---|---|---|
|
MRCIEU/TwoSampleMR-v0.5.7.zip
md5:ebd941896f03f7ead07384c507325064 |
3.0 MB | Download |
1,139
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downloads
| All versions | This version | |
|---|---|---|
| Views | 1,139 | 3 |
| Downloads | 148 | 0 |
| Data volume | 886.3 MB | 0 Bytes |
| Unique views | 1,054 | 3 |
| Unique downloads | 117 | 0 |
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- Publication date:
- May 29, 2023
- DOI:
-
- Related identifiers:
- Supplement to
- License (for files):
- MIT License