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Check overlap with XGR annotations

Source: R/XGR_iterate_overlap.R
XGR_iterate_overlap.Rd

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 (XGR on CRAN). Passed to the RData.customised argument in XGR::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(), XGR_enrichment_bootstrap(), XGR_enrichment_plot(), 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

if (FALSE) { # \dontrun{
gr.hits <- XGR_iterate_overlap(
    lib.selections = c("ENCODE_TFBS_ClusteredV3_CellTypes"),
    dat = echodata::BST1
)
} # }