ROADMAP_query: Query Roadmap Query Roadmap annotations using a set of...

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

Query Roadmap Query Roadmap annotations using a set of genomic coordinates.

Description

Query Roadmap

Query Roadmap annotations using a set of genomic coordinates.

Usage

ROADMAP_query(
  query_dat,
  keyword_query = NULL,
  limit_files = NULL,
  chrom_states = NULL,
  n_top = NULL,
  min_hits = 1,
  save_dir = file.path(tempdir(), paste(paste0("roadmap_query--", paste(keyword_query,
    collapse = "-")), paste0("n_top--", n_top), paste0("limit_files--", limit_files),
    paste(chrom_states, collapse = "-"), sep = ".")),
  force_new = FALSE,
  return_paths = FALSE,
  merge_and_process = FALSE,
  conda_env = "echoR_mini",
  nThread = 1,
  verbose = TRUE
)

Arguments

query_dat	Variant-level summary statistics.
keyword_query	Search all columns in the Roadmap annotations metadata and only query annotations that contain your keywords. Can provide multiple keywords in list form: c("placenta","liver","monocytes").
limit_files	Limit the number of annotation files queried (for faster testing).
chrom_states	Filter results by chromatin states.
n_top	The number of top annotation sources (e.g. tissues) to include, sorted by greatest number of rows (i.e. the number of genomic ranges within the window).
min_hits	Minimum number of hits (regions overlapping with query_dat) required to include a given annotation.
save_dir	Directory to store query results in.
force_new	Overwrite any existing files of the same name.
return_paths	Return list of paths instead of a GRangesList.
merge_and_process	Perform filtering and merging of GRangesList items.
conda_env	Conda environment to search for tabix in.
nThread	Number of threads to parallelise queries over.
verbose	Print messages.

See Also

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

Examples

query_dat <- echodata::BST1
grl <- ROADMAP_query(
    query_dat = query_dat,
    keyword_query = "monocyte")

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