Search ROADMAP annotation reference for GoShifter — GOSHIFTER_search_ROADMAP • echoannot

Search the ROADMAP Epigenomic reference file for annotation BED files matching filter criteria or a fuzzy keyword search.

Usage

GOSHIFTER_search_ROADMAP(
  Roadmap_reference = system.file("extdata/ROADMAP", "ROADMAP_Epigenomic.js", package =
    "echoannot"),
  EID_filter = NA,
  GROUP_filter = NA,
  ANATOMY_filter = NA,
  GR_filter = NA,
  fuzzy_search = NA,
  verbose = TRUE
)

Arguments

Roadmap_reference: Path to the ROADMAP reference file (default: bundled file in echoannot).
EID_filter: Filter by Epigenome ID(s).
GROUP_filter: Filter by GROUP column.
ANATOMY_filter: Filter by ANATOMY column.
GR_filter: Filter by GR column.
fuzzy_search: Keyword(s) to search across all annotation columns (case-insensitive).
verbose: Print messages (default TRUE).

Value

A data.table of matching ROADMAP annotation entries.

See also

Other GOSHIFTER: GOSHIFTER(), GOSHIFTER_bed_names(), GOSHIFTER_check_overlap(), GOSHIFTER_create_LD(), GOSHIFTER_create_snpmap(), GOSHIFTER_find_folder(), GOSHIFTER_get_roadmap_annotations(), GOSHIFTER_heatmap(), GOSHIFTER_histograms_SNPgroups(), GOSHIFTER_histograms_pvals(), GOSHIFTER_list_chromatin_states(), GOSHIFTER_process_results(), GOSHIFTER_run(), GOSHIFTER_summarise_results()