Introduction | Installation | Quick Start | Locate example files | Read variant information | Convert PGEN to GDS | Explore the GDS file | Access genotype data | Advanced Usage | Selecting a subset of variants | Importing a range with start/count | Parallel conversion | Conversion from GDS to PGEN | Integration with Bioconductor | Cleanup | Session Info
Package: pgen2gds 0.99.4
Xiuwen Zheng
pgen2gds: Format Conversion between PLINK2 PGEN and GDS
Provides functions to convert files from the PLINK2 pgen format to SeqArray GDS, and from SeqArray GDS to the PLINK2 pgen format.
Authors:
pgen2gds_0.99.4.tar.gz
pgen2gds_0.99.4.zip(r-4.7-x86_64)pgen2gds_0.99.4.zip(r-4.7-arm64)pgen2gds_0.99.4.zip(r-4.6-x86_64)pgen2gds_0.99.4.zip(r-4.6-arm64)pgen2gds_0.99.4.zip(r-4.5-x86_64)
pgen2gds_0.99.4.tgz(r-4.6-x86_64)pgen2gds_0.99.4.tgz(r-4.6-arm64)pgen2gds_0.99.4.tgz(r-4.5-x86_64)pgen2gds_0.99.4.tgz(r-4.5-arm64)
pgen2gds_0.99.4.tar.gz(r-4.7-arm64)pgen2gds_0.99.4.tar.gz(r-4.7-x86_64)pgen2gds_0.99.4.tar.gz(r-4.6-arm64)pgen2gds_0.99.4.tar.gz(r-4.6-x86_64)
pgen2gds_0.99.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pgen2gds/json (API)
| # Install 'pgen2gds' in R: |
| install.packages('pgen2gds', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zhengxwen/pgen2gds/issues
On BioConductor:pgen2gds-0.99.4(bioc 3.24)
infrastructuredataimportgeneticsgdsplinkcpp
Last updated from:0988b4a999. Checks:4 NOTE, 12 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 128 | ||
| linux-devel-arm64 | OK | 156 | ||
| linux-devel-x86_64 | OK | 206 | ||
| source / vignettes | OK | 169 | ||
| linux-release-arm64 | OK | 167 | ||
| linux-release-x86_64 | OK | 278 | ||
| macos-release-arm64 | OK | 129 | ||
| macos-release-x86_64 | OK | 496 | ||
| macos-oldrel-arm64 | NOTE | 156 | ||
| macos-oldrel-x86_64 | NOTE | 341 | ||
| windows-devel-arm64 | OK | 255 | ||
| windows-devel-x86_64 | OK | 217 | ||
| windows-release-arm64 | OK | 272 | ||
| windows-release-x86_64 | OK | 130 | ||
| windows-oldrel-x86_64 | NOTE | 153 | ||
| wasm-release | OK | 93 |
Exports:seqGDS2PGENseqPGEN2GDSseqReadPVAR
Dependencies:BiocGenericsBiostringscrayondigestgdsfmtgenericsGenomicRangesIRangespgenlibrRcppS4VectorsSeqArraySeqinfoXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert SeqArray GDS to PLINK2 PGEN files | seqGDS2PGEN |
| Reformat PLINK2 PGEN files | seqPGEN2GDS |
| Read PLINK2 pvar file | seqReadPVAR |