Package: SNPkit 0.1.0

Vinícius Junqueira

SNPkit: S4 Tools for Reading and Organizing Genetic Data

Provides an integrated suite of tools for handling single nucleotide polymorphism (SNP) genotype data in large-scale genetic studies. Supports importing and merging genotype files, performing quality control on SNP markers and samples, and preparing data for downstream analyses using popular software such as 'FImpute' and 'PLINK'. Offers S4 classes and methods to efficiently encapsulate SNP data, along with utilities for generating genotype summary statistics and visualization. Additional functionalities include anticlustering approaches for batch effect control, automated script generation for external software, and streamlined workflows for large datasets commonly encountered in animal and plant breeding programs. Designed to facilitate reproducible and scalable SNP data analyses in quantitative and statistical genetics.

Authors:Vinícius Junqueira [aut, cre], Roberto Higa [aut], Fernando Flores Cardoso [aut], Marcos Jun Iti Yokoo [aut]

SNPkit_0.1.0.tar.gz
SNPkit_0.1.0.tar.gz(r-4.7-arm64)SNPkit_0.1.0.tar.gz(r-4.7-x86_64)SNPkit_0.1.0.tar.gz(r-4.6-arm64)SNPkit_0.1.0.tar.gz(r-4.6-x86_64)
SNPkit_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SNPkit/json (API)

# Install 'SNPkit' in R:

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

Bug tracker:https://github.com/viniciusjunqueira/snpkit/issues

Pkgdown/docs site:https://viniciusjunqueira.github.io

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

2.70 score 1 scripts 47 exports 40 dependencies

Last updated from:f97312921d. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	173
linux-devel-x86_64	OK	188
source / vignettes	OK	200
linux-release-arm64	OK	192
linux-release-x86_64	OK	179
wasm-release	OK	152

Exports:as_snpmatrix cbind_SnpMatrix check.call.rate check.ibs check.identical.samples check.identical.samples.by.block check.mendelian.inconsistencies check.mendelian.inconsistencies.pair check.sample.call.rate check.sample.heterozygosity check.snp.chromo check.snp.hwe check.snp.hwe.chi2 check.snp.maf check.snp.mgf check.snp.monomorf check.snp.no.position check.snp.same.position combineSNPData doPCA exploratory.plots FImputeRunner genoToDF get.correl.fc get.gender get.hwe.chi2 getGeno ibs.pair import_geno_list importAllGenos importFImputeResults pairs2sets plotPCAgroups qc_header qcSamples qcSNPs rbind_SnpMatrix rbindSnpFlexible read.fimpute run_admixture runAnticlusteringPCA runFImpute saveFImpute saveFImputeRaw savePlink Subset summary

Dependencies:anticlust BiocGenerics cli cpp11 data.table dplyr farver generics ggplot2 glue gtable isoband labeling lattice lifecycle lpSolve magrittr MASS Matrix pillar pkgconfig plyr R6 RANN RColorBrewer Rcpp reshape2 rlang S7 scales snpStats stringi stringr survival tibble tidyselect utf8 vctrs viridisLite withr

Getting started with SNPkit

Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2026-06-26
Started: 2026-06-26

Help page	Topics
Convert a genotype matrix or data.frame to snpStats::SnpMatrix	as_snpmatrix
Safe cbind for SnpMatrix preserving dimnames	cbind_SnpMatrix
Check SNP call rate	check.call.rate
Check Identity-By-State (IBS) for a genotype pair	check.ibs
Check identical samples based on distance	check.identical.samples
Check identical samples by block	check.identical.samples.by.block
Check Mendelian inconsistencies	check.mendelian.inconsistencies
Check Mendelian inconsistencies for a pair	check.mendelian.inconsistencies.pair
Check Sample Call Rate	check.sample.call.rate
Check sample heterozygosity	check.sample.heterozygosity
Check SNP by chromosome	check.snp.chromo
Check SNP Hardy-Weinberg equilibrium deviation	check.snp.hwe
Check SNPs for Hardy-Weinberg equilibrium deviation using chi-square p-values	check.snp.hwe.chi2
Check SNP minor allele frequency	check.snp.maf
Check SNP missing genotype frequencies	check.snp.mgf
Check SNP monomorphic status	check.snp.monomorf
Check SNP no position	check.snp.no.position
Check SNPs mapped to the same position	check.snp.same.position
Combine multiple SNPDataLong objects	combineSNPData
Do genome relationship matrix PCA	doPCA
Exploratory plots for SNP and sample summary	exploratory.plots
FImputeExport Class	FImputeExport-class
Build FImputeRunner object	FImputeRunner
FImputeRunner Class	FImputeRunner-class
Convert geno slot from SNPDataLong to a data.frame	genoToDF
Get correlation (fc method)	get.correl.fc
Get gender based on heterozygosity	get.gender
Get HWE chi-square p-values	get.hwe.chi2
Flexible and efficient genotype file reading with autodetection using fread	getGeno getGeno,ANY-method
IBS pair statistics	ibs.pair
Import multiple genotype datasets from a list of configurations	import_geno_list
Import and combine multiple genotype configurations	importAllGenos importAllGenos,SNPImportList-method
Import imputed FImpute results from disk	importFImputeResults
Convert pairs to sets	pairs2sets
Plot PCA groups from anticlustering result	plotPCAgroups
Print method for SNPDataLong summary	print.summary.SNPDataLong
Formatted header message	qc_header
Quality control on samples	qcSamples qcSamples,SNPDataLong-method
Quality Control for SNPDataLong with optional criteria	qcSNPs qcSNPs,SNPDataLong-method
Safe rbind for SnpMatrix preserving dimnames	rbind_SnpMatrix
Faster row-bind for SnpMatrix objects with differing columns	rbindSnpFlexible
Read imputed genotypes from FImpute output and return SNPDataLong object	read.fimpute
Run ADMIXTURE analysis	run_admixture
Run PCA and anticlustering on SNPDataLong	runAnticlusteringPCA
Run FImpute from a FImputeRunner object	runFImpute runFImpute,FImputeRunner-method
Save genotype and map files in FImpute format	saveFImpute saveFImpute,FImputeExport-method saveFImpute,SNPDataLong-method
Export genotypes and map using basic arguments	saveFImputeRaw
Save SNPDataLong object to PLINK format	savePlink
SNPFileConfig Class	SNPFileConfig-class
SNPImportList Class	SNPImportList-class
Subset an SNPDataLong object	Subset Subset,SNPDataLong-method
Summary for SNPDataLong objects	summary,SNPDataLong-method

Package: SNPkit 0.1.0

SNPkit: S4 Tools for Reading and Organizing Genetic Data

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