Package: Rpgen 0.1.0

Sounkou Mahamane Toure

Rpgen: PLINK 2 Genotype Ingestion into File-Backed Storage

Uses the 'PLINK 2' pgenlib library and its native importers (<https://github.com/chrchang/plink-ng>) to ingest PGEN, PLINK 1 BED, PED/MAP, TPED/TFAM, VCF/BCF, BGEN, Oxford GEN, HAPS/legend, EIGENSTRAT, and legacy dosage sources into bounded, file-backed 'Rfmalloc' layouts. Hardcalls, dosages, and phase are transferred as typed record panels, allowing the destination to choose a packed codec or full-precision storage without constructing a complete R matrix. The vendored native readers are also exposed through 'R_RegisterCCallable' for sibling packages.

Authors:Sounkou Mahamane Toure [aut, cre], Christopher Chang [cph], Shaun Purcell [cph], Eric Biggers [cph], Yann Collet [cph], Meta Platforms, Inc. [cph], Evan Nemerson [cph], Mutsuo Saito [cph], Makoto Matsumoto [cph]

Rpgen_0.1.0.tar.gz
Rpgen_0.1.0.zip(r-4.7)Rpgen_0.1.0.zip(r-4.6)Rpgen_0.1.0.zip(r-4.5)
Rpgen_0.1.0.tgz(r-4.6-x86_64)Rpgen_0.1.0.tgz(r-4.6-arm64)Rpgen_0.1.0.tgz(r-4.5-x86_64)Rpgen_0.1.0.tgz(r-4.5-arm64)
Rpgen_0.1.0.tar.gz(r-4.7-arm64)Rpgen_0.1.0.tar.gz(r-4.7-x86_64)Rpgen_0.1.0.tar.gz(r-4.6-arm64)Rpgen_0.1.0.tar.gz(r-4.6-x86_64)
Rpgen_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rpgen/json (API)

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

Bug tracker:https://github.com/sounkou-bioinfo/rfmalloc/issues

Uses libs:
  • libzstd– Fast lossless compression algorithm
  • libdeflate– Fast, whole-buffer DEFLATE-based compression and decompression
  • zlib– Compression library

On CRAN:

Conda:

altrepblasgenomicsggmlggufllmllm-inferencemallocmemory-mappedmmapout-of-corequantizationsimdlibzstdlibdeflatezlib

3.08 score 4 stars 19 exports 1 dependencies

Last updated from:6e05ad0361. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK146
linux-devel-x86_64OK163
source / vignettesOK294
linux-release-arm64OK157
linux-release-x86_64OK149
macos-release-arm64OK136
macos-release-x86_64OK276
macos-oldrel-arm64OK153
macos-oldrel-x86_64OK332
windows-develOK258
windows-releaseOK236
windows-oldrelOK209
wasm-releaseOK146

Exports:rpgen_bedrpgen_bed_inforpgen_dosagerpgen_haplotypesrpgen_import_bcfrpgen_import_bedrpgen_import_bgenrpgen_import_eigenstratrpgen_import_genrpgen_import_hapsrpgen_import_pedrpgen_import_plink1_dosagerpgen_import_tpedrpgen_import_vcfrpgen_inforpgen_ingestrpgen_read_bed_hardcallsrpgen_read_dosagesrpgen_read_hardcalls

Dependencies:Rfmalloc