annotate_consequences: Annotate with consequences

In matmu/MouseFM: In-silico methods for genetic finemapping in inbred mice

Annotate with consequences

Description

Request variant consequences from Variant Effect Predictor (VEP) via Ensembl Rest Service. Not recommended for large queries.

Usage

annotate_consequences(geno, species)

Arguments

geno	Data frame or GenomicRanges::GRanges object including columns rsid, ref, alt.
species	Species name, e.g. mouse (GRCm38) or human (GRCh38).

Value

Data frame.

Examples

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")

matmu/MouseFM documentation built on Sept. 3, 2022, 5:46 a.m.