Download and subset ROADMAP annotations for GoShifter

Download ROADMAP chromHMM BED files from the WashU Epigenome Browser, optionally subset to a specific chromatin state, and return paths to the processed files.

Usage

GOSHIFTER_get_roadmap_annotations(
  annotations_path = "./annotations",
  bed_list,
  chromatin_state = "TssA",
  verbose = TRUE
)

Arguments

annotations_path

Directory where annotation files are stored/cached.

bed_list

Character vector of BED file names (as produced by GOSHIFTER_bed_names).

chromatin_state

Chromatin state to subset by (e.g. "TssA"). Set to NA to keep all states.

verbose

Print messages (default TRUE).

Value

A character vector of paths to processed BED files (gzipped).

See also

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