ROADMAP_tabix: Query Roadmap API

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

Query Roadmap API

Description

Query Roadmap epigenomic annotations (chromatin marks) using a range of genomic coordinates.

Usage

ROADMAP_tabix(
  eid,
  query_dat,
  save_dir = tempdir(),
  force_new = FALSE,
  conda_env = "echoR_mini",
  nThread = 1,
  verbose = TRUE
)

Arguments

eid	Roadmap annotation ID
query_dat	Variant-level summary statistics.
save_dir	Directory to store query results in.
force_new	Overwrite any existing files of the same name.
verbose	Print messages.
as_granges	Whether to return query as a data.frame or GRanges.

Details

ROADMAP file locations.

Source

query_dat <- echodata::BST1 dat <- ROADMAP_tabix( query_dat = query_dat, eid = "E099")

See Also

Other ROADMAP: ROADMAP_construct_reference(), ROADMAP_merge_and_process(), ROADMAP_query()

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.