Package: gwasvcf 0.1.6

Gibran Hemani

gwasvcf: Tools for Dealing with GWAS Summary Data in VCF Format

Tools for dealing with GWAS summary data in VCF format. Includes reading, querying, writing, as well as helper functions such as LD proxy searches.

Authors:Gibran Hemani [aut, cre], Tom Palmer [ctb], Rita Rasteiro [ctb]

gwasvcf_0.1.6.tar.gz
gwasvcf_0.1.6.zip(r-4.7)gwasvcf_0.1.6.zip(r-4.6)gwasvcf_0.1.6.zip(r-4.5)
gwasvcf_0.1.6.tgz(r-4.6-any)gwasvcf_0.1.6.tgz(r-4.5-any)
gwasvcf_0.1.6.tar.gz(r-4.7-any)gwasvcf_0.1.6.tar.gz(r-4.6-any)
gwasvcf_0.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gwasvcf/json (API)

# Install 'gwasvcf' in R:

install.packages('gwasvcf', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrcieu/gwasvcf/issues

Pkgdown/docs site:https://mrcieu.github.io

On CRAN:

7.20 score 105 stars 166 scripts 33 exports 83 dependencies

Last updated from:53daf45a1e. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	375
source / vignettes	OK	277
linux-release-x86_64	OK	367
macos-release-arm64	OK	274
macos-oldrel-arm64	OK	265
windows-devel	OK	332
windows-release	OK	382
windows-oldrel	OK	286
wasm-release	OK	143

Exports:%>%check_bcftools check_plink create_ldref_sqlite create_pval_index_from_vcf create_rsidx_index_from_vcf create_rsidx_sub_index create_vcf get_ld_proxies gwasvcf_to_summaryset merge_vcf parse_chrompos proxy_match query_chrompos_bcftools query_chrompos_file query_chrompos_vcf query_gwas query_pval_bcftools query_pval_file query_pval_sqlite3 query_pval_vcf query_pvali query_rsid_bcftools query_rsid_file query_rsid_rsidx query_rsid_vcf query_rsidx set_bcftools set_plink sqlite_ld_proxies vcf_to_granges vcf_to_tibble vcflist_overlaps

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl data.table DBI DelayedArray dplyr fastmap formatR futile.logger futile.options generics genetics.binaRies GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue gwasglue2 httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 VariantAnnotation vctrs withr XML XVector yaml

Reading, querying and writing GWAS summary data in VCF format

Rendered fromguide.Rmdusingknitr::rmarkdown

Last update: 2025-06-06
Started: 2019-11-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check if the tools_bcftools option is set	check_bcftools
Check if the tools_plink option is set	check_plink
Create LD reference sqlite database for tags	create_ldref_sqlite
Create pval index from GWAS-VCF file	create_pval_index_from_vcf
Create RSID index from VCF	create_rsidx_index_from_vcf
Create new index from existing index using a subset of rsids	create_rsidx_sub_index
Create GWAS vcf	create_vcf
Find LD proxies for a set of SNPs	get_ld_proxies
Create a SummarySet	gwasvcf_to_summaryset
Merge two GWAS VCF objects	merge_vcf
Parse chromosome:position	parse_chrompos
Extract SNPs from vcf file	proxy_match
Query chromosome and position using bcftools	query_chrompos_bcftools
Query vcf file, extracting by chromosome and position	query_chrompos_file
Query chrompos from vcf object	query_chrompos_vcf
Query data from vcf file	query_gwas
Query p-value using bcftools	query_pval_bcftools
Query pval from vcf file	query_pval_file
Query pval from file using pvali index	query_pval_sqlite3
Query based on p-value threshold from vcf	query_pval_vcf
Query pvali	query_pvali
Query	query_rsid_bcftools
Query vcf file, extracting by rsid	query_rsid_file
Query rsid from file using rsidx index	query_rsid_rsidx
Query rsid from vcf object	query_rsid_vcf
Query rsidx	query_rsidx
Set bcftools binary location	set_bcftools
Set plink binary location	set_plink
Lookup LD proxies from sqlite database	sqlite_ld_proxies
VariantAnnotation	VariantAnnotation
Convert vcf format to granges format	vcf_to_granges
Convert vcf format to tibble (data frame)	vcf_to_tibble
Reduce list of VCFs to intersecting regions	vcflist_overlaps