rain 0.7.1

chore(DESCRIPTION): update email address.

Full Changelog: https://github.com/umr1283/rain/compare/v0.7.0...v0.7.1

rain 0.7.0

Fix digits = 0 in format() no longer supported in R >4.2.0.
Fix CI workflows not using latest GitHub Actions and pak.
Fix Remotes field of DESCRIPTION to use "local" flashpcaR.

rain 0.6.0

Minor text improvements

In R/compute_pca.R,
- Fix typos.
- Major figure upgrade.R

rain 0.5.1

Minor text improvements

In R/pca_report.R,
- Remove unnecessary lower condition for outliers.
- Update obsolete captions.
- Perform independent association testing between technical variables and principal components.
- Order association plot according to pvalues and principal components.
In R/compute_pca.R,
- Fix explained variance histogram.

rain 0.5.0

Breaking Changes

In R/pca_report.R,
- Code refactoring using data.table.
In R/compute_pca.R,
- Code refactoring using data.table.
- Tweak ethnicity figure.
- Add an ethnicity figure focussing on the studied cohort.

rain 0.4.1

Minor text improvements

In R/pca_report.R,
- Change text for outliers in the last part of the PCA report.

rain 0.4.0

Minor improvements and fixes

In DESCRIPTION,
- Use patchwork for ethnicity plot.
- Remove gcta64 from system requirements.
In R/compute_pca.R,
- Use R.utils to count number of SNPs from *.bim file.
- Fix number of SNPs in ggplot legend.
- Fix a missplaced .data pronoun.
- Core code rewrite.
- Change messages prefix.
In R/pca_report.R,
- Add packages prefix for tidyselect.
- Update to ggplot2 v3.3.0.

rain 0.3.0

Minor improvements and fixes

Remove covr.
Remove testthat.

rain 0.2.0

New features

pca_report() allows to compute an analysis report using principal component analysis from flashpca tool.
The function can be used in a chunk within a Rmarkdown document/script with results="asis" to render the report (from CARoT v0.4.0).

rain 0.1.0

New features

estimate_ethnicity() allows to format VCF files and compute the genomic components (and some figures) for ethnicity. (CARoT v0.4.0)