portal_query: Search and download fine-mapping files
In RajLabMSSM/echodata: echoverse module: Fine-mapping data access and formatting

portal_query

R Documentation

Search and download fine-mapping files

Description

Search the echolocatoR Fine-mapping Portal for fine-mapping results, LD, and locus plots.

Usage

portal_query(
  dataset_types = NULL,
  datasets = NULL,
  phenotypes = NULL,
  file_types = c("multi_finemap", "LD", "plot"),
  loci = NULL,
  LD_panels = c("UKB", "1KGphase1", "1KGphase3"),
  results_dir = tempdir(),
  overwrite = FALSE,
  as_datatable = FALSE,
  nThread = 1,
  verbose = TRUE
)

Arguments

`dataset_types`	Dataset types to search for (e.g. "GWAS", "QTL").
`datasets`	Dataset names to search for (e.g. "Ripke_2014", "Wray_2018").
`phenotypes`	Phenotypes to search for (e.g. "Schizophrenia", "Major Depressive Disorder").
`file_types`	File types to search for: "multi_finemap":Fine-mapping results merged with GWAS/QTL summary statistics. "LD":Linkage Disequilibrium with the lead SNP in each locus. "plot" : Locus plots of fine-mapped results.
`loci`	Locus names to search for (e.g. "BST1", "CHRNB1", "LRRK2").
`LD_panels`	LD panels to search for, or results generated using different LD panels (e.g. "UKB", "1KGphase1", "1KGphase3").
`results_dir`	Where to save the matching queries.
`overwrite`	Whether to overwrite previously saved queries with the same names.
`as_datatable`	Return results organized in a data.table. Otherwise, will return a list of local file paths.
`nThread`	Number of threads to parallelise downloads across.
`verbose`	Print messages.

Value

List of local paths where the requested files were downloaded to.

Examples

local_finemap <- portal_query(
    dataset_types = "GWAS",
    phenotypes = c("schizophrenia", "parkinson"),
    file_types = "multi_finemap",
    loci = c("BST1", "CHRNB1", "LRRK2"),
    LD_panels="1KGphase3")

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.