IEU tables conversion to GRanges

ieutab_to_GRanges(ieutab, build = "GRCh37")

Arguments

ieutab: data.frame-like entity as returned by e.g., variant_rsid, associations, phewas
build: character(1) defaults to "GRCh37"

Note

assumes SNP; renames 'pos' to 'position' if necessary

Examples

if (requireNamespace("ieugwasr")) {
ex = ieugwasr::variants_rsid("rs6060535")
ieutab_to_GRanges(ex)
}
#> GRanges object with 1 range and 24 metadata columns:
#>       seqnames    ranges strand |       query        name         chr  position
#>          <Rle> <IRanges>  <Rle> | <character> <character> <character> <integer>
#>   [1]       20  34235522      * |   rs6060535   rs6060535          20  34235522
#>          geneinfo         MUS          U5          U3         MSM         ASS
#>       <character> <character> <character> <character> <character> <character>
#>   [1]  CPNE1:8904           .           .           .           .           .
#>               VLD         NSF      COMMON         PMC          PM          R5
#>       <character> <character> <character> <character> <character> <character>
#>   [1]           .           .           1           1           1           .
#>                VC         TPA          R3         DSS dbSNPBuildID          OM
#>       <character> <character> <character> <character>  <character> <character>
#>   [1]           .           .           .           .            .           .
#>               INT         SYN
#>       <character> <character>
#>   [1]           1           .
#>   -------
#>   seqinfo: 1 sequence from GRCh37 genome; no seqlengths