Function reference • gwasvcf

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

Reference

All functions