Background | Case 1: Genotype imputation accuracy | Case 2: Genotype concordance | Case 3: Phasing switch error | Case 4: Multiple testing repetitively | Q&A | Where is the allele frequency from and can I use customized one? | How to fix the error "inconsistent samples name" | NA values returned
Package: vcfppR 0.8.3
vcfppR: Rapid Manipulation of the Variant Call Format (VCF)
The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Authors:
vcfppR_0.8.3.tar.gz
vcfppR_0.8.3.zip(r-4.7)vcfppR_0.8.3.zip(r-4.6)vcfppR_0.8.3.zip(r-4.5)
vcfppR_0.8.3.tgz(r-4.6-x86_64)vcfppR_0.8.3.tgz(r-4.6-arm64)vcfppR_0.8.3.tgz(r-4.5-x86_64)vcfppR_0.8.3.tgz(r-4.5-arm64)
vcfppR_0.8.3.tar.gz(r-4.7-arm64)vcfppR_0.8.3.tar.gz(r-4.7-x86_64)vcfppR_0.8.3.tar.gz(r-4.6-arm64)vcfppR_0.8.3.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
vcfppR/json (API)
| # Install 'vcfppR' in R: |
| install.packages('vcfppR', repos = c('https://zilong-li.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zilong-li/vcfppr/issues
Uses libs:
bioinformaticsfastrhtslibpopulation-geneticspopulation-genomicsvcfvcf-datavisulizationzlibbzip2xz-utilscurllibdeflatecpp
Last updated from:2c9a33b0fa. Checks:6 OK, 6 NOTE, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 180 | ||
| linux-devel-x86_64 | OK | 238 | ||
| source / vignettes | OK | 294 | ||
| linux-release-arm64 | OK | 189 | ||
| linux-release-x86_64 | OK | 195 | ||
| macos-release-arm64 | OK | 180 | ||
| macos-release-x86_64 | NOTE | 428 | ||
| macos-oldrel-arm64 | NOTE | 209 | ||
| macos-oldrel-x86_64 | NOTE | 492 | ||
| windows-devel | NOTE | 293 | ||
| windows-release | NOTE | 290 | ||
| windows-oldrel | NOTE | 240 | ||
| wasm-release | FAIL | 103 |
Exports:plot_variants_per_haplotypevcfcompvcfinfovcfplotvcfpopgenvcfpp_calc_info_persitevcfreadervcfsummaryvcftablevcfwriter
Dependencies:Rcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| vcfppR: Rapid Manipulation of the Variant Call Format (VCF) | vcfppR-package vcfppR |
| Plot variants on haplotypes across multiple samples | plot_variants_per_haplotype |
| Subset a vcftable object | subset.vcftable |
| Compare two VCF/BCF files reporting various statistics | vcfcomp |
| read a INFO tag in the VCF/BCF into R data structure | vcfinfo |
| Make sensible and beautiful plots based on various objects in vcfppR | vcfplot |
| count the heterozygous sites per sample in the VCF/BCF | vcfpopgen |
| Calculate INFO score from GP after genotype imputation | vcfpp_calc_info_persite |
| API for manipulating the VCF/BCF. | vcfreader |
| summarize the various variant types at both variant level and sample level. | vcfsummary |
| read VCF/BCF contents into R data structure | vcftable |
| API for writing the VCF/BCF. | vcfwriter |
