fetch_tabix: Query eQTL Catalogue:tabix/echotabix

In RajLabMSSM/catalogueR: QTL data extraction and colocalization

Query eQTL Catalogue:tabix/echotabix

Description

Query eQTL Catalogue datasets by region with tabix or echotabix. Faster alternative to REST API.

Usage

fetch_tabix(
  unique_id,
  query_granges,
  query_method = c("rsamtools", "variantannotation", "conda", "seqminer"),
  quant_method = "ge",
  nThread = 1,
  conda_env = "echoR_mini",
  verbose = TRUE
)

Arguments

query_granges	GRanges object to be used for querying the target_path file. Alternatively, can be variant-level summary statistics to be converted into a GRanges object by construct_query.
query_method	Method used for querying. See query for available options.
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"
nThread	The number of CPU cores you want to use to speed up your queries through parallelization.
conda_env	Conda environment to search for tabix executable in.
verbose	Show more (=TRUE) or fewer (=FALSE) messages.

Source

eQTL Catalogue blocking tabix requests

data("meta"); query_granges <- echotabix::construct_query(query_dat = echodata::BST1) qtl.subset <- catalogueR:::fetch_tabix(unique_id=meta$unique_id[2], query_granges=query_granges)

See Also

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

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