get_qtls: Query Qtlizer

In matmu/qtlizer: Comprehensive QTL annotation of GWAS results

Query Qtlizer

Description

Query Qtlizer database for expression quantitative trait loci (eQTLs) in human.

Usage

get_qtls(query, corr = NA, max_terms = 5, ld_method = "r2",
  ref_version = "hg19", return_obj = "dataframe")

Arguments

query	The query consists of search terms and can be a single string or a vector. Qtlizer allows to query both variants (Rsid, ref_version:chr:pos) and genes (Symbol consisting of letters and numbers according to the HGNC guidelines). Minimum allowed term length is 2.
corr	Linkage disequilibrium based on 1000 Genomes Phase 3 European. If this optional value between 0 and 1 is set, the input variants are enriched for proxy variants passing the threshold. Default value is NA.
max_terms	Number of terms in a single HTTP request. Default value is 5. A large value can lead to a very large result set and a error by the database.
ld_method	There are two methods available: "r2" (default) and "dprime".
ref_version	Two possible versions are supported: hg19 (GRCh37) or hg38 (GRCh38). Default value is "hg19". This argument is only considered if a GenomicRanges::GRanges object is returned.
return_obj	The user can choose to get the QTL data to be returned as data frame or as a GenomicRanges::GRanges object. The default value is "dataframe".

Value

Data frame or GenomicRanges::GRanges object containing QTL data.

Examples

get_qtls("rs4284742")
get_qtls(c("rs4284742", "DEFA1"))
get_qtls("rs4284742,DEFA1")
get_qtls("rs4284742", return_obj="granges", ref_version="hg38")
get_qtls("rs4284742", corr=0.6)

matmu/qtlizer documentation built on March 29, 2022, 12:03 p.m.