Package: smartsnp 1.1.0

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_1.1.0.tar.gz
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smartsnp_1.1.0.tgz(r-4.4-x86_64)smartsnp_1.1.0.tgz(r-4.4-arm64)smartsnp_1.1.0.tgz(r-4.3-x86_64)smartsnp_1.1.0.tgz(r-4.3-arm64)
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smartsnp.pdf |smartsnp.html✨
smartsnp/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

5.32 score 7 stars 5 scripts 242 downloads 5 exports 45 dependencies

Last updated 10 months agofrom:01e53da532. Checks:OK: 1 NOTE: 5 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-win-x86_64NOTEOct 25 2024
R-4.5-linux-x86_64NOTEOct 25 2024
R-4.4-win-x86_64NOTEOct 25 2024
R-4.4-mac-x86_64NOTEOct 25 2024
R-4.4-mac-aarch64NOTEOct 25 2024
R-4.3-win-x86_64WARNINGOct 25 2024
R-4.3-mac-x86_64WARNINGOct 25 2024
R-4.3-mac-aarch64WARNINGOct 25 2024

Exports:read_packedancestrymapsmart_mvasmart_pcasmart_permanovasmart_permdisp

Dependencies:bitbit64bootSVDcliclustercodetoolscpp11crayondata.tablefansiffforeachgluehmsiteratorslatticelifecyclemagrittrMASSMatrixmgcvnlmepermutepillarpkgconfigprettyunitsprogressR6RcppRcppArmadilloRcppEigenRcppGSLRcppParallelRcppZigguratRfastrlangRSpectratibbletidyselecttzdbutf8vctrsveganvroomwithr

Example PCA, PERMANOVA and PERMDISP analysis

Rendered frommallard_smartpca_analysis.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2021-06-19
Started: 2021-06-07

Projecting ancient samples

Rendered fromaDNA_smartpca_analysis.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2021-06-19
Started: 2021-06-12

Using VCF and PLINK formatted files with smartsnp

Rendered fromConverting_VCF_and_PLINK_formats.Rmdusingknitr::rmarkdownon Oct 25 2024.

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