KRIS
(Keen and Reliable Interface Subroutines for
bioinformatic analysis) is the package providing 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..
You can install the released version of KRIS from CRAN with:
install.packages("KRIS")
Alternatively, you can install the dev version of KRIS from Gitlab with
install.packages("remotes")
remotes::install_github("kridsadakorn/kris", dependencies = TRUE)
You can see the reference manual from: https://www.biostatgen.org/kris/
This is a basic example which shows you how to use the package:
library(KRIS)
data(example_SNP)
example_SNP
consists of the simulated SNP data simsnp
and the sample
labels sample_labels
.
summary(simsnp)
#> Length Class Mode
#> snp 206000 -none- numeric
#> snp.info 6 data.frame list
#> ind.info 6 data.frame list
summary(sample_labels)
#> Length Class Mode
#> 103 character character
To calcualte the first three linear principal components from SNP data:
PCs <- cal.pc.linear(simsnp$snp, no.pc = 3)
You can visualize 3 dimensions for the first three principal components as: