Description Usage Arguments Value Examples
Request variant consequences from Variant Effect Predictor (VEP) via Ensembl Rest Service. Not recommended for large queries.
1 | annotate_consequences(geno, species)
|
geno |
Data frame or GenomicRanges::GRanges object including columns rsid, ref, alt. |
species |
Species name, e.g. mouse (GRCm38) or human (GRCh38). |
Data frame.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | geno = finemap("chr1",
start = 5000000, end = 6000000,
strain1 = c("C57BL_6J"), strain2 = c("AKR_J", "A_J", "BALB_cJ")
)
df = annotate_consequences(geno[seq_len(10), ], "mouse")
geno.granges = finemap("chr1",
start = 5000000, end = 6000000,
strain1 = c("C57BL_6J"), strain2 = c("AKR_J", "A_J", "BALB_cJ"),
return_obj = "granges"
)
df2 = annotate_consequences(geno.granges[seq_len(10), ], "mouse")
|
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