Package index • 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 from file using pvali index

query_pval_vcf(): Query based on p-value threshold from vcf

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