Package: KRIS 1.1.6

Kridsadakorn Chaichoompu

KRIS: Keen and Reliable Interface Subroutines for Bioinformatic Analysis

Provides useful functions which are needed for bioinformatic analysis such as calculating linear principal components from numeric data and Single-nucleotide polymorphism (SNP) dataset, calculating fixation index (Fst) using Hudson method, creating scatter plots in 3 views, handling with PLINK binary file format, detecting rough structures and outliers using unsupervised clustering, and calculating matrix multiplication in the faster way for big data.

Authors:Kridsadakorn Chaichoompu [aut, cre], Kristel Van Steen [aut], Fentaw Abegaz [aut], Sissades Tongsima [aut], Philip James Shaw [aut], Anavaj Sakuntabhai [aut], Luisa Pereira [aut]

KRIS_1.1.6.tar.gz
KRIS_1.1.6.tar.gz(r-4.5-noble)KRIS_1.1.6.tar.gz(r-4.4-noble)
KRIS_1.1.6.tgz(r-4.4-emscripten)KRIS_1.1.6.tgz(r-4.3-emscripten)
KRIS.pdf |KRIS.html✨
KRIS/json (API)
NEWS

# Install 'KRIS' in R:

install.packages('KRIS', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

sample_labels - Synthetic dataset containing population labels for the dataset simsnp.
simsnp - Synthetic dataset containing single nucleotide polymorphisms

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.73 score 2 packages 18 scripts 206 downloads 1 mentions 9 exports 6 dependencies

Last updated 4 years agofrom:ac8c515667. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-linux	OK	Nov 19 2024

Exports:cal.pc.linear cal.pc.projection fst.each.snp.hudson fst.hudson plot3views read.bed rubikclust write.bed xxt

Dependencies:lattice Matrix rARPACK Rcpp RcppEigen RSpectra

Help page	Topics
Calculate linear principal component analysis (PCA) from numeric data and Single-nucleotide polymorphism (SNP) dataset	cal.pc.linear
Calculate linear principal component analysis (PCA) with a projection method for Single-nucleotide polymorphism (SNP) dataset.	cal.pc.projection
Calculate the fixation index (Fst) for all SNPs between two groups of individuals from Single-nucleotide polymorphism (SNP)	fst.each.snp.hudson
Calculate the average fixation index (Fst) between two groups of individuals from Single-nucleotide polymorphism (SNP)	fst.hudson
Create scatter plots in three views.	plot3views
Read the binary PLINK format (BED, BIM, and FAM)	read.bed
(Internal) Replace missing values with other values,internally used for parallelization	replace.missing
Unsupervised clustering to detect rough structures and outliers.	rubikclust
Synthetic dataset containing population labels for the dataset simsnp.	sample_labels
Synthetic dataset containing single nucleotide polymorphisms (SNP)	simsnp
Write a list of SNP object to the binary PLINK format (BED, BIM, and FAM)	write.bed
Calculate matrix multipication between a matrix and its transpose for large data.	xxt

Package: KRIS 1.1.6

KRIS: Keen and Reliable Interface Subroutines for Bioinformatic Analysis

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)