Installation | Introduction | Meta | How to use the functions of this package | Parallel processing (optional) | Load VCF and associated files of individuals and groups | Assessment of missing data | Basic stats for individuals in VCF | Filtering, subsetting, merging and otherwise wrangling VCF files | Subsetting samples and variants | Filtering | Extracting and binding | Filtering with outgroup | Saving and copying VCFArrow objects | Converting a VCF file to other population genetic and phylogenetic formats
Package: VCFArrow 0.9.0
Tomas Hrbek
VCFArrow: Fast and Memory-Efficient Manipulation and Conversion of VCF Files
Reads Variant Call Format (VCF) files into an S4 object whose genotypes are stored on disk as an 'Apache Arrow' dataset and loaded lazily, allowing large datasets to be processed with little memory. Provides functions to filter variants and samples, subset and merge datasets, compute summary statistics and diagnostic plots, write VCF files, and convert data to input formats of population genetic and phylogenetic software such as 'STRUCTURE', 'ADMIXTURE', 'PLINK', 'EIGENSTRAT', 'Arlequin', 'GENEPOP', 'BayeScan', 'TreeMix', 'SNAPP' and 'adegenet'.
Authors:
VCFArrow_0.9.0.tar.gz
VCFArrow_0.9.0.zip(r-4.7-x86_64)VCFArrow_0.9.0.zip(r-4.7-arm64)VCFArrow_0.9.0.zip(r-4.6-x86_64)VCFArrow_0.9.0.zip(r-4.6-arm64)VCFArrow_0.9.0.zip(r-4.5-x86_64)
VCFArrow_0.9.0.tgz(r-4.6-x86_64)VCFArrow_0.9.0.tgz(r-4.6-arm64)VCFArrow_0.9.0.tgz(r-4.5-x86_64)VCFArrow_0.9.0.tgz(r-4.5-arm64)
VCFArrow_0.9.0.tar.gz(r-4.7-arm64)VCFArrow_0.9.0.tar.gz(r-4.7-x86_64)VCFArrow_0.9.0.tar.gz(r-4.6-arm64)VCFArrow_0.9.0.tar.gz(r-4.6-x86_64)
VCFArrow_0.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
VCFArrow/json (API)
| # Install 'VCFArrow' in R: |
| install.packages('VCFArrow', repos = c('https://legallab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/legallab/vcfarrow/issues
Pkgdown/docs site:https://legallab.github.io
Last updated from:922263f7f2. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 139 | ||
| linux-devel-x86_64 | OK | 169 | ||
| source / vignettes | OK | 262 | ||
| linux-release-arm64 | OK | 146 | ||
| linux-release-x86_64 | OK | 171 | ||
| macos-release-arm64 | OK | 161 | ||
| macos-release-x86_64 | OK | 359 | ||
| macos-oldrel-arm64 | OK | 194 | ||
| macos-oldrel-x86_64 | OK | 317 | ||
| windows-devel-arm64 | OK | 415 | ||
| windows-devel-x86_64 | OK | 187 | ||
| windows-release-arm64 | OK | 405 | ||
| windows-release-x86_64 | OK | 118 | ||
| windows-oldrel-x86_64 | OK | 153 | ||
| wasm-release | OK | 131 |
Exports:assess_vcf_coverageassess_vcf_missing_dataread_vcfset_vcf_groupsshowvcf_bindvcf_bind_sparsevcf_copyvcf_extract_groupsvcf_extract_samplesvcf_filter_adrvcf_filter_biallelicvcf_filter_coveragevcf_filter_hetsvcf_filter_indelsvcf_filter_invariantvcf_filter_mafvcf_filter_missingvcf_filter_missingnessvcf_filter_multiSNVvcf_filter_oneSNVvcf_filter_paralogsvcf_filter_passvcf_filter_qualityvcf_filter_rankvcf_filter_rptvcf_gcvcf_memory_estimatevcf_set_workersvcf_statsvcf_sub_SNVsvcf_sub_SNVs_stratifiedvcf_suggest_chunk_sizevcf_thetavcf2admixturevcf2apparentvcf2arlequinvcf2bayesassvcf2bayescanvcf2eigenstratvcf2fastavcf2fineradstructurevcf2genepopvcf2genlightvcf2gt_longvcf2migratevcf2nexusvcf2plink_bedvcf2plink_pedvcf2relatedvcf2smartsnpvcf2snappvcf2snmfvcf2structurevcf2treemixwrite_vcf
Dependencies:arrowassertthatbitbit64clicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerRcpprlangS7scalesstringistringrtibbletidyselectutf8vctrsviridisLitewithr
