NEWS.md

In KRIS: Keen and Reliable Interface Subroutines for Bioinformatic Analysis

title: "NEWS" author: "Kridsadakorn Chaichoompu" date: "10/05/2019" output: html_document: keep_md: yes toc: yes pdf_document: number_sections: yes toc: yes word_document: toc: yes

KRIS 1.1.6

• Update 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 1.1.1

• 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 1.0.3

• 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 1.0.0.0

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.

KRIS documentation built on Jan. 21, 2021, 5:08 p.m.