XGR_enrichment: XGR enrichment

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

XGR enrichment

Description

Run SNP-level enrichment test with xGRviaGenomicAnno.

Usage

XGR_enrichment(
  gr,
  merged_dat,
  foreground_filter = "Consensus_SNP==TRUE",
  background_filter = NULL,
  grouping_vars = c("Study", "Assay", "Cell_type"),
  fg_sample_size = NULL,
  bg_sample_size = NULL,
  background.annotatable.only = FALSE,
  verbose = TRUE
)

Arguments

gr	Annotations to test for enrichment with.
merged_dat	SNP-level fine-mapping results to test for enrichment with.
foreground_filter	Filter to apply to foreground (target SNPs).
background_filter	Filter to apply to background (non-target SNPs).
grouping_vars	Columns in merged_dat to group by when conducting enrichment tests.
fg_sample_size	Foreground sample size.
bg_sample_size	Background sample size.
background.annotatable.only	For background SNPs, only use SNPs that overlap with some annotation in gr. This means that missing annotations (NA) will not be considered.
verbose	Print messages.

See Also

Other XGR: XGR_enrichment_bootstrap(), XGR_enrichment_plot(), 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_query(), XGR_sep_handler(), xgr_example

Examples

## Not run: 
gr.merged <- echoannot::merge_celltype_specific_epigenomics()
enrich.lead <- XGR_enrichment(
    gr = gr.merged,
    merged_dat = echodata::get_Nalls2019_merged(),
    foreground_filter = "leadSNP==TRUE",
    grouping_vars = c("Study", "Cell_type", "Assay")
)

## End(Not run)

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