locStra
Fast Implementation of (Local) Population Stratification Methods
Description
Fast implementations to compute the genetic covariance matrix, the Jaccard similarity matrix, the s-matrix (the weighted Jaccard similarity matrix), and the (classic or robust) genomic relationship matrix of a (dense or sparse) input matrix (see Hahn, Lutz, Hecker, Prokopenko, Cho, Silverman, Weiss, and Lange (2020) <doi:10.1002/gepi.22356>). Full support for sparse matrices from the R-package 'Matrix'. Additionally, an implementation of the power method (von Mises iteration) to compute the largest eigenvector of a matrix is included, a function to perform an automated full run of global and local correlations in population stratification data, a function to compute sliding windows, and a function to invert minor alleles and to select those variants/loci exceeding a minimal cutoff value. New functionality in locStra allows one to extract the k leading eigenvectors of the genetic covariance matrix, Jaccard similarity matrix, s-matrix, and genomic relationship matrix via fast PCA without actually computing the similarity matrices. The fast PCA to compute the k leading eigenvectors can now also be run directly from 'bed'+'bim'+'fam' files.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (14 non-OK)
CRAN incoming feasibility
Maintainer: ‘Georg Hahn <ghahn@hsph.harvard.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Georg",
family = "Hahn",
role = c("aut", "cre"),
email = "ghahn@hsph.harvard.edu"),
person(given = c("Sharon", "M."),
family = "Lutz",
role = "ctb"),
person(given = "Christoph",
family = "Lange",
role = "ctb"))
as necessary.
CRAN incoming feasibility
Maintainer: ‘Georg Hahn <ghahn@hsph.harvard.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Georg",
family = "Hahn",
role = c("aut", "cre"),
email = "ghahn@hsph.harvard.edu"),
person(given = c("Sharon", "M."),
family = "Lutz",
role = "ctb"),
person(given = "Christoph",
family = "Lange",
role = "ctb"))
as necessary.
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installed package size
installed size is 27.9Mb
sub-directories of 1Mb or more:
libs 27.8Mb
installed package size
installed size is 28.5Mb
sub-directories of 1Mb or more:
libs 28.4Mb
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Check History
NOTE 10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
CRAN incoming feasibility
Maintainer: ‘Georg Hahn <ghahn@hsph.harvard.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Georg",
family = "Hahn",
role = c("aut", "cre"),
email = "ghahn@hsph.harvard.edu"),
person(given = c("Sharon", "M."),
family = "Lutz",
role = "ctb"),
person(given = "Christoph",
family = "Lange",
CRAN incoming feasibility
Maintainer: ‘Georg Hahn <ghahn@hsph.harvard.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Georg",
family = "Hahn",
role = c("aut", "cre"),
email = "ghahn@hsph.harvard.edu"),
person(given = c("Sharon", "M."),
family = "Lutz",
role = "ctb"),
person(given = "Christoph",
family = "Lange",
installed package size
installed size is 27.9Mb
sub-directories of 1Mb or more:
libs 27.8Mb
installed package size
installed size is 28.5Mb
sub-directories of 1Mb or more:
libs 28.4Mb