xgr_query: Download, standardize, and merge XGR annotations

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

Download, standardize, and merge XGR annotations

Description

Merges a list of XGR annotations into a single GRangesList (or merged GRanges) object.

Usage

XGR_query(
  lib.selections = c("ENCODE_TFBS_ClusteredV3_CellTypes", "TFBS_Conserved",
    "Uniform_TFBS"),
  as_grangesList = FALSE,
  dat = NULL,
  n_top = NULL,
  nThread = 1
)

Arguments

lib.selections	Which XGR annotations to check overlap with. For full list of libraries see here. Passed to the RData.customised argument in xRDataLoader.
as_grangesList	Return as a GRangesList, instead of a single merged GRanges object.
dat	data.table of genomic coordinates to query with. Set as NULL to return genome-wide data.
n_top	Filter to only the top N annotations that have the greatest amount of overlap with the genomic coordinates of dat.
nThread	Number of cores to parallelise across.

Value

GRangesList

See Also

Other XGR: XGR_enrichment_bootstrap(), XGR_enrichment_plot(), XGR_enrichment(), XGR_filter_assays(), XGR_filter_sources(), XGR_import_annotations(), XGR_iterate_enrichment(), XGR_iterate_overlap(), XGR_merge_and_process(), XGR_parse_metadata(), XGR_plot_enrichment(), XGR_prepare_foreground_background(), XGR_sep_handler(), xgr_example

Examples

gr.lib <- echoannot::XGR_query(
    lib.selections = c("ENCODE_DNaseI_ClusteredV3_CellTypes"),
    dat = echodata::BST1, 
    n_top = 1)

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