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Conduct enrichment tests for each annotation

Source: R/XGR_iterate_enrichment.R
XGR_iterate_enrichment.Rd

XGR uses a binomial enrichment tests for each annotation.

Usage

XGR_iterate_enrichment(
  dat,
  foreground_filter = "Consensus_SNP",
  background_filter = "leadSNP",
  lib.selections = c("ENCODE_TFBS_ClusteredV3_CellTypes",
    "ENCODE_DNaseI_ClusteredV3_CellTypes", "Broad_Histone", "FANTOM5_Enhancer",
    "Segment_Combined_Gm12878", "TFBS_Conserved", "ReMap_PublicAndEncode_TFBS",
    "Blueprint_VenousBlood_Histone", "Blueprint_DNaseI", "FANTOM5_CAT_Cell",
    "FANTOM5_CAT_MESH", "GWAScatalog_alltraits"),
  save_path = FALSE,
  nThread = 1
)

Arguments

dat

Data.frame with at least the following columns:

SNP

SNP RSID

CHR

chromosome

POS

position

foreground_filter

Specify foreground by filtering SNPs in dat. Write filter as a string (or NULL to include all SNPs).

background_filter

Specify background by filtering SNPs in dat. Write filter as a string (or NULL to include all SNPs).

Details

Description of all datasets

See also

Other XGR: XGR_enrichment(), XGR_enrichment_bootstrap(), XGR_enrichment_plot(), XGR_filter_assays(), XGR_filter_sources(), XGR_import_annotations(), XGR_iterate_overlap(), 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{
enrich_res <- XGR_iterate_enrichment(
    dat = echodata::get_Nalls2019_merged(),
    foreground_filter = "Consensus_SNP",
    background_filter = "leadSNP",
    lib.selections = c("ENCODE_TFBS_ClusteredV3_CellTypes")
)
} # }