Changelog

Source: NEWS.md

KRIS 1.1.7

  • Updated the reference with DOI in Description file
  • Updated Markdown files
  • extra on Gitlab, document page pkgdown::build_site()
  • extra on Gitlab, add use_gitlab_ci()

KRIS 1.1.62021-01-21

  • Updated the packages according to R v4.0.0

KRIS 1.1.5

  • Add the function to calculate pvalue from 2 different groups using regression model and allowing to correct for covariates
  • Change the way to call function and fixed bugs for plot3views

KRIS 1.1.4

  • Fixed some incorrect descriptions in the manual.

KRIS 1.1.3

  • Fixed bugs in plot3views for mismatching color and pattern on a plot

KRIS 1.1.2

  • Fixed bugs in read.bed

KRIS 1.1.12018-06-04

  • Updated and added more examples in plot3view

KRIS 1.1.0

  • Added the function cal.pc.projection
  • Moved replace.missing to for_parallel.R from principal.component.R
  • Fixed bugs in test_plot3views.R

KRIS 1.0.4

  • Changed URL in the CITATION file from Gitlab to CRAN
  • Changed email in the DESCRIPTION file from Gmail to Official email
  • Fixed misspelling in a manual of data

KRIS 1.0.32018-05-07

  • Updated URLs and added details of package in the DESCRIPTION file
  • Updated manual of all functions according from CRAN’s comments

KRIS 1.0.2

  • Fixed the help file for read.bed, read.bed, fst.each.snp.hudson and fst.hudson.

KRIS 1.0.1

  • Fixed the help file for cal.pc.linear and rubikclust.

KRIS 1.0.0

Initial functions

  • cal.pc.linear A function for linear principal component analysis (PCA)
  • fst.each.snp.hudson A function for fixation index (Fst) calculation for all SNPs between two groups.
  • fst.hudson A function for average fixation index (Fst) calculation between two groups.
  • plot3views A function to create scatter plots in three views.
  • read.bed Read the binary PLINK format (BED, BIM, and FAM)
  • rubikclust A function for unsupervised clustering to detect rough structures and outliers.
  • write.bed Write an list of SNP object to the binary PLINK format (BED, BIM, and FAM)
  • xxt A function for calculating matrix multipication between a matrix and its transpose for large data.

Initial R data

  • simsnp Synthetic dataset containing single nucleotide polymorphisms (SNP)
  • sample_labels Synthetic dataset containing population labels for the dataset simsnp.

Initial example files

  • example_SNP.bed Synthetic dataset containing single nucleotide polymorphisms (SNP) in binary format
  • example_SNP.bim Simulated SNP information
  • example_SNP.fam Simulated sample information

Updates

From the initial idea, some functions were changed their names:

  • The name of function cal.PC.linear was changed to cal.pc.linear.
  • The name of function plot.3views was changed to plot3views.
  • The name of function rubikClust was changed to rubikclust.
  • The name of function XXt was changed to xxt.