Turn a gwas_data object or data.frame into a Bioconductor
GRanges object, with association statistics stored as
metadata columns, for interoperability with the Bioconductor ecosystem
(e.g. VariantAnnotation, SummarizedExperiment, coloc).
Arguments
- x
A
gwas_dataobject or a data.frame accepted byas_gwas_data().- ...
Column overrides passed to
as_gwas_data()whenxis a plain data.frame.
Value
A GRanges object, one width-1 range per variant, named by SNP when available.
Examples
data(example_gwas)
gr <- as_granges(example_gwas)
gr
#> GRanges object with 8000 ranges and 7 metadata columns:
#> seqnames ranges strand | SNP P BETA
#> <Rle> <IRanges> <Rle> | <character> <numeric> <numeric>
#> rs2678525 16 80841579 * | rs2678525 0.18988331 -0.01723
#> rs8451246 5 80011524 * | rs8451246 0.05264044 -0.02073
#> rs7069507 12 34577737 * | rs7069507 0.04506835 0.01575
#> rs4824759 12 16869788 * | rs4824759 0.00680649 -0.10267
#> rs7209949 7 38647669 * | rs7209949 0.56527788 -0.00012
#> ... ... ... ... . ... ... ...
#> rs7761398 11 23750379 * | rs7761398 0.115608 0.05872
#> rs7135121 3 69639436 * | rs7135121 0.929757 0.04248
#> rs6635611 18 40340076 * | rs6635611 0.788155 0.06943
#> rs6641483 13 74927676 * | rs6641483 0.174590 0.00629
#> rs5502842 20 14803036 * | rs5502842 0.291328 0.06330
#> SE A1 A2 AF
#> <numeric> <character> <character> <numeric>
#> rs2678525 0.01314 G T 0.2522
#> rs8451246 0.01070 G T 0.3089
#> rs7069507 0.00786 T A 0.3404
#> rs4824759 0.03794 C A 0.1418
#> rs7209949 0.00021 T C 0.3506
#> ... ... ... ... ...
#> rs7761398 0.03732 C G 0.1445
#> rs7135121 0.48192 T C 0.3549
#> rs6635611 0.25838 G A 0.3425
#> rs6641483 0.00463 T A 0.2657
#> rs5502842 0.05999 C T 0.1301
#> -------
#> seqinfo: 22 sequences from an unspecified genome; no seqlengths
# Round-trip back to gwas_data
as_gwas_data(gr)
#> A gwas_data object: 8,000 variants across 22 chromosomes
#> Min p-value: 1.19e-14
#> Lambda GC: 3.996
#> Columns: CHR, BP, SNP, P, BETA, SE, A1, A2, AF