07/32: gnu: Add r-snprelate.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 46cae56dfe63ca72b5aaf38c28275b6109d9a572
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Jul 19 14:53:06 2023 +0200

    gnu: Add r-snprelate.
    
    * gnu/packages/bioconductor.scm (r-snprelate): New variable.
---
 gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9d924c5429..f6917405a3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -20025,6 +20025,41 @@ segmented data for individual and multiple arrays.")
     ;; Expanded from GPL
     (license (list license:gpl2+ license:gpl3+))))
 
+(define-public r-snprelate
+  (package
+    (name "r-snprelate")
+    (version "1.34.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "SNPRelate" version))
+              (sha256
+               (base32
+                "0js932qvhlwmnrr2jfvsch2zm6w6a1z5wydns3r1bw24r817dlgh"))))
+    (properties `((upstream-name . "SNPRelate")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-gdsfmt))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/zhengxwen/SNPRelate";)
+    (synopsis
+     "Toolset for relatedness and Principal Component Analysis of SNP data")
+    (description
+     "Genome-wide association studies (GWAS) are widely used to investigate
+the genetic basis of diseases and traits, but they pose many computational
+challenges.  The R package SNPRelate provides a binary format for
+single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic
+Data Structure (GDS) data files.  The GDS format offers the efficient
+operations specifically designed for integers with two bits, since a SNP could
+occupy only two bits.  SNPRelate is also designed to accelerate two key
+computations on SNP data using parallel computing for multi-core symmetric
+multiprocessing computer architectures: Principal Component Analysis (PCA) and
+relatedness analysis using Identity-By-Descent measures.  The SNP GDS format
+is also used by the GWASTools package with the support of S4 classes and
+generic functions.  The extended GDS format is implemented in the SeqArray
+package to support the storage of single nucleotide variations (SNVs),
+insertion/deletion polymorphism (indel) and structural variation calls in
+whole-genome and whole-exome variant data.")
+    (license license:gpl3)))
+
 (define-public r-snpstats
   (package
     (name "r-snpstats")