fetch_restAPI: 2. Query eQTL Catalogue datasets by region

In RajLabMSSM/catalogueR: QTL data extraction and colocalization

2. Query eQTL Catalogue datasets by region

Description

2.2 Method 2: RESTful API Slower than tabix (unless you're only querying several specific SNPs).

Usage

fetch_restAPI(
  unique_id,
  query_granges,
  quant_method = "ge",
  is_gwas = FALSE,
  size = NULL,
  timeout = 5 * 60,
  verbose = TRUE
)

Arguments

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"

verbose

Show more (=TRUE) or fewer (=FALSE) messages.

Source

data("meta") query_granges <- echotabix::construct_query(query_dat = echodata::BST1) qtl.subset <- fetch_restAPI(unique_id = meta$unique_id[1], query_granges = query_granges)

See Also

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

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