annotate_consequences: Annotate with consequences

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

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")

MouseFM documentation built on Nov. 8, 2020, 7:26 p.m.