get_variant: Get associations for a given variant

In rqtl/GWASapi: NHGRI-EBI GWAS Catalog of Summary Statistics

Description

Get all associations for a given variant

Usage

get_variant(rsnum, chr = NULL, p_lower = NULL, p_upper = NULL,
  study = NULL, start = NULL, size = NULL)

Arguments

rsnum	RS number for a variant
chr	chromosome number if known
p_lower	Lower bound on p-values
p_upper	Upper bound of p-values
study	Restrict to a particular study
start	First record to retrieve (starting at 0)
size	Maximum number of results to retrieve

Value

Data frame with associations as rows

See Also

get_asso(), get_trait_asso()

Examples

# get associations for a given variant
results <- get_variant("rs2228603")
# use information about the chromosome it's on
results <- get_variant("rs2228603", 19)
# get the next 20 results
next20 <- get_variant("rs2228603", 19, start=20)
# get 100 results rather than just 20
first100 <- get_variant("rs2228603", 19, size=100)
# return just the associations with P < 1e-8
top_results <- get_variant("rs2228603", 19, p_upper=1e-8)

rqtl/GWASapi documentation built on Nov. 5, 2019, 4:15 a.m.