XGR_iterate_enrichment: Conduct enrichment tests for each annotation

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

Conduct enrichment tests for each annotation

Description

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_bootstrap(), XGR_enrichment_plot(), XGR_enrichment(), 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

## Not run: 
enrich_res <- XGR_iterate_enrichment(
    dat = echodata::get_Nalls2019_merged(),
    foreground_filter = "Consensus_SNP",
    background_filter = "leadSNP",
    lib.selections = c("ENCODE_TFBS_ClusteredV3_CellTypes")
)

## End(Not run)

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