eQTLcatalogue_fetch: Query eQTL Catalogue

In RajLabMSSM/catalogueR: QTL data extraction and colocalization

Query eQTL Catalogue

Description

Query eQTL Catalogue datasets with multiple methods options.

Usage

eQTLcatalogue_fetch(
  unique_id,
  query_granges,
  method = c("REST", "tabix"),
  quant_method = "ge",
  multithread_tabix = FALSE,
  add_qtl_id = TRUE,
  convert_genes = TRUE,
  suffix = ".QTL",
  timeout = 5 * 60,
  conda_env = "echoR_mini",
  nThread = 1,
  verbose = TRUE
)

Arguments

unique_id	Unique eQTL Catalogue ID assigned in metadata ("unique_id" column in data(meta)).
method	Method for querying eQTL Catalogue: "REST" (default): Uses the REST API. Slow but can be used by anyone. "tabix"Uses tabix query. Fast, but requires the user to first get their IP address whitelisted by the EMBL-EBI server admin by putting in a request here. Note: "tabix" is about ~17x faster than the REST API, but is currently a far less reliable method than the REST API because tabix tends to get blocked by eQTL Catalogue's firewall. See here for more details.
quant_method	eQTL Catalogue actually contains more than just eQTL data. For each dataset, the following kinds of QTLs can be queried: gene expression QTL quant_method="ge" (default) or quant_method="microarray", depending on the dataset. catalogueR will automatically select whichever option is available. exon expression QTL *under construction* quant_method="ex" transcript usage QTL *under construction* quant_method="tx" promoter, splice junction and 3' end usage QTL *under construction* quant_method="txrev"
multithread_tabix	Multi-thread across within a single tabix file query (good when you have one-several large loci).
add_qtl_id	Add "qtl_id" (i.e. "unique_id") column to the query result.
convert_genes	Convert Ensembl IDs to HGNC symbols.
conda_env	Conda environment to search for tabix executable in.
nThread	The number of CPU cores you want to use to speed up your queries through parallelization.
verbose	Show more (=TRUE) or fewer (=FALSE) messages.
query_dat	data.table of GWAS summary statistics.
chrom	Chromosome of the query window.
bp_lower	Minimum basepair position of the query window.
bp_upper	Maxmimum basepair position of the query window.

See Also

Other eQTL Catalogue: eQTLcatalogue_header, eQTLcatalogue_iterate_fetch(), eQTLcatalogue_query(), eQTLcatalogue_search_metadata(), fetch_restAPI(), fetch_tabix(), merge_gwas_qtl(), meta

Examples

data("meta")
query_granges <- echodata::BST1
GWAS.QTL_manual <- catalogueR::eQTLcatalogue_fetch(
  query_granges = query_granges,
  unique_id = meta$unique_id[1])

RajLabMSSM/catalogueR documentation built on Jan. 1, 2023, 10:45 a.m.