Package: gwasvcf 0.1.2

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_0.1.2.tar.gz
gwasvcf_0.1.2.zip(r-4.5)gwasvcf_0.1.2.zip(r-4.4)gwasvcf_0.1.2.zip(r-4.3)
gwasvcf_0.1.2.tgz(r-4.4-any)gwasvcf_0.1.2.tgz(r-4.3-any)
gwasvcf_0.1.2.tar.gz(r-4.5-noble)gwasvcf_0.1.2.tar.gz(r-4.4-noble)
gwasvcf_0.1.2.tgz(r-4.4-emscripten)gwasvcf_0.1.2.tgz(r-4.3-emscripten)
gwasvcf.pdf |gwasvcf.html✨
gwasvcf/json (API)
NEWS

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

Peer review:

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

On CRAN:

33 exports 66 stars 5.73 score 84 dependencies 2 dependents 91 scripts

Last updated 1 years agofrom:477b365da8. Checks:ERROR: 2 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesFAILSep 24 2024
R-4.5-winWARNINGSep 24 2024
R-4.5-linuxERRORSep 24 2024
R-4.4-winWARNINGSep 24 2024
R-4.4-macWARNINGSep 24 2024
R-4.3-winWARNINGSep 24 2024
R-4.3-macWARNINGSep 24 2024

Exports:%>%check_bcftoolscheck_plinkcreate_ldref_sqlitecreate_pval_index_from_vcfcreate_rsidx_index_from_vcfcreate_rsidx_sub_indexcreate_vcfget_ld_proxiesgwasvcf_to_summarysetmerge_vcfparse_chromposproxy_matchquery_chrompos_bcftoolsquery_chrompos_filequery_chrompos_vcfquery_gwasquery_pval_bcftoolsquery_pval_filequery_pval_sqlite3query_pval_vcfquery_pvaliquery_rsid_bcftoolsquery_rsid_filequery_rsid_rsidxquery_rsid_vcfquery_rsidxset_bcftoolsset_plinksqlite_ld_proxiesvcf_to_grangesvcf_to_tibblevcflist_overlaps

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydplyrfansifastmapformatRfutile.loggerfutile.optionsgenericsgenetics.binaRiesGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluegwasglue2httrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLXVectoryamlzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Check if the tools_bcftools option is setcheck_bcftools
Check if the tools_plink option is setcheck_plink
Create LD reference sqlite database for tagscreate_ldref_sqlite
Create pval index from GWAS-VCF filecreate_pval_index_from_vcf
Create RSID index from VCFcreate_rsidx_index_from_vcf
Create new index from existing index using a subset of rsidscreate_rsidx_sub_index
Create GWAS vcfcreate_vcf
Find LD proxies for a set of SNPsget_ld_proxies
Create a SummarySetgwasvcf_to_summaryset
Merge two GWAS VCF objectsmerge_vcf
Parse chromosome:positionparse_chrompos
Extract SNPs from vcf fileproxy_match
Query chromosome and position using bcftoolsquery_chrompos_bcftools
Query vcf file, extracting by chromosome and positionquery_chrompos_file
Query chrompos from vcf objectquery_chrompos_vcf
Query data from vcf filequery_gwas
Query p-value using bcftoolsquery_pval_bcftools
Query pval from vcf filequery_pval_file
Query pval from file using pvali indexquery_pval_sqlite3
Query based on p-value threshold from vcfquery_pval_vcf
Query pvaliquery_pvali
Queryquery_rsid_bcftools
Query vcf file, extracting by rsidquery_rsid_file
Query rsid from file using rsidx indexquery_rsid_rsidx
Query rsid from vcf objectquery_rsid_vcf
Query rsidxquery_rsidx
Set bcftools binary locationset_bcftools
Set plink binary locationset_plink
Lookup LD proxies from sqlite databasesqlite_ld_proxies
VariantAnnotationVariantAnnotation
Convert vcf format to granges formatvcf_to_granges
Convert vcf format to tibble (data frame)vcf_to_tibble
Reduce list of VCFs to intersecting regionsvcflist_overlaps