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.
The R package
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.
The R package
KRIS requires the package
Here is the list of functions in the R package
Moreover, here is the list of example datasets in the R package
Install the released version of
KRIS from CRAN:
The source codes in this package include the Roxgen's syntax. If there is a
problem for generating the RD files (facing some errors) using RStudio (Build >
Document), try to use
roxygen2::roxygenise() instead of Build > Document
from the menu. Alternatively, install the package
devtools, then enable
RStudio to use the functions from
devtools (check Build > Configure Build
Tools... > use devtools package functions if available) or run
devtools::document() in the console.
When facing error for
testthat, try to update the package
testthat and add
Suggests: testthat in DESCRIPTION file.
Check the submission using
R CMD check --as-cran and a current version of
r-devel, as mandated by the CRAN Repository Policy. (You could do so using the
win-builder service at http://win-builder.r-project.org)
Check downstream dependencies with
Edit ~/.profile, ~/.bash_profile or ~/.bashrc, then add
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replace.missingto for_parallel.R from principal.component.R
cal.pc.linearA function for linear principal component analysis (PCA)
fst.each.snp.hudsonA function for fixation index (Fst) calculation for all SNPs between two groups.
fst.hudsonA function for average fixation index (Fst) calculation between two groups.
plot3viewsA function to create scatter plots in three views.
read.bedRead the binary PLINK format (BED, BIM, and FAM)
rubikclustA function for unsupervised clustering to detect rough structures and outliers.
write.bedWrite an list of SNP object to the binary PLINK format (BED, BIM, and FAM)
xxtA function for calculating matrix multipication between a matrix and its transpose for large data.
simsnpSynthetic dataset containing single nucleotide polymorphisms (SNP)
sample_labelsSynthetic dataset containing population labels for the dataset simsnp.
example_SNP.bedSynthetic dataset containing single nucleotide polymorphisms (SNP) in binary format
example_SNP.bimSimulated SNP information
example_SNP.famSimulated sample information
From the initial idea, some functions were changed their names:
cal.PC.linearwas changed to
plot.3viewswas changed to
rubikClustwas changed to
XXtwas changed to