NEWS.md

In omicsr/rain: Reference-based Ancestry INference

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)

omicsr/rain documentation built on Nov. 28, 2022, 8:36 a.m.