Package: smartsnp 1.2.1

smartsnp: Fast Multivariate Analyses of Big Genomic Data

Fast computation of multivariate analyses of small (10s to 100s markers) to big (1000s to 100000s) genotype data. Runs Principal Component Analysis allowing for centering, z-score standardization and scaling for genetic drift, projection of ancient samples to modern genetic space and multivariate tests for differences in group location (Permutation-Based Multivariate Analysis of Variance) and dispersion (Permutation-Based Multivariate Analysis of Dispersion).

Authors:Salvador Herrando-Perez [aut], Ray Tobler [ctb], Christian Huber [ctb, cre]

smartsnp_1.2.1.tar.gz
smartsnp_1.2.1.zip(r-4.7-x86_64)smartsnp_1.2.1.zip(r-4.7-arm64)smartsnp_1.2.1.zip(r-4.6-x86_64)smartsnp_1.2.1.zip(r-4.6-arm64)smartsnp_1.2.1.zip(r-4.5-x86_64)
smartsnp_1.2.1.tgz(r-4.6-x86_64)smartsnp_1.2.1.tgz(r-4.6-arm64)smartsnp_1.2.1.tgz(r-4.5-x86_64)smartsnp_1.2.1.tgz(r-4.5-arm64)
smartsnp_1.2.1.tar.gz(r-4.7-arm64)smartsnp_1.2.1.tar.gz(r-4.7-x86_64)smartsnp_1.2.1.tar.gz(r-4.6-arm64)smartsnp_1.2.1.tar.gz(r-4.6-x86_64)
smartsnp_1.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
smartsnp/json (API)

# Install 'smartsnp' in R:
install.packages('smartsnp', repos = c('https://christianhuber.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/christianhuber/smartsnp/issues

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

5.98 score 7 stars 23 scripts 533 downloads 5 exports 43 dependencies

Last updated from:3389463394. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK121
linux-devel-x86_64OK155
source / vignettesOK206
linux-release-arm64OK125
linux-release-x86_64OK129
macos-release-arm64OK135
macos-release-x86_64OK293
macos-oldrel-arm64OK140
macos-oldrel-x86_64OK247
windows-devel-arm64OK389
windows-devel-x86_64OK165
windows-release-arm64OK383
windows-release-x86_64OK137
windows-oldrel-x86_64OK125
wasm-releaseOK110

Exports:read_packedancestrymapsmart_mvasmart_pcasmart_permanovasmart_permdisp

Dependencies:bitbit64bootSVDcliclustercodetoolscpp11crayondata.tableffforeachgluehmsiteratorslatticelifecyclemagrittrMASSMatrixmgcvnlmepermutepillarpkgconfigprettyunitsprogressR6RcppRcppArmadilloRcppEigenRcppParallelRfastrlangRSpectratibbletidyselecttzdbutf8vctrsveganvroomwithrzigg

Example PCA, PERMANOVA and PERMDISP analysis
Description of the data | Install package smartsnp (use one option) | Load package | Create group factor | Run smart_pca | Run smart_permanova | Run smart_permdisp | Run smart_mva
Rendered frommallard_smartpca_analysis.Rmdusingknitr::rmarkdown

Last update: 2025-06-10
Started: 2021-06-07

Projecting ancient samples
Install package smartsnp | Downloading the data | Select subsets of individuals with convertf | Merging ancient with modern data using mergeit | Running smartpca | Plotting the results using ggplot2
Rendered fromaDNA_smartpca_analysis.Rmdusingknitr::rmarkdown

Last update: 2025-06-10
Started: 2021-06-12

Using VCF and PLINK formatted files with smartsnp
Download a small example VCF | VCF to PLINK (.bed) | PLINK to raw genotype (.traw) | VCF to raw genotype (.traw) | Running smartpca
Rendered fromConverting_VCF_and_PLINK_formats.Rmdusingknitr::rmarkdown

Last update: 2021-06-23
Started: 2021-06-13