XGR_iterate_overlap: Check overlap with XGR annotations

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

Check overlap with XGR annotations

Description

Automatically handles different file formats provided by XGR (e.g. varying kinds of nested/unnested GRanges). Then returns a Granges object with only the XGR annotation ranges that overlap with the SNPs in dat. The GRanges merges hits from dat.

Usage

XGR_iterate_overlap(
  lib.selections = c("ENCODE_TFBS_ClusteredV3_CellTypes", "TFBS_Conserved",
    "ReMap_PublicAndEncode_TFBS", "Uniform_TFBS"),
  dat,
  save_path = FALSE,
  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.
dat	Data.frame with at least the following columns: SNP SNP RSID CHR chromosome POS position
save_path	Save the results as a data.frame.
nThread	Number of threads to parallelise across libraries.

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_merge_and_process(), XGR_parse_metadata(), XGR_plot_enrichment(), XGR_prepare_foreground_background(), XGR_query(), XGR_sep_handler(), xgr_example

Examples

## Not run: 
gr.hits <- XGR_iterate_overlap(
    lib.selections = c("ENCODE_TFBS_ClusteredV3_CellTypes"),
    dat = echodata::BST1
)

## End(Not run)

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