XGR_prepare_foreground_background: Prepare SNP sets for enrichment

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

Prepare SNP sets for enrichment

Description

Prepare custom foreground and background SNPs sets for enrichment tests with XGR annotations.

Usage

XGR_prepare_foreground_background(
  dat,
  foreground_filter = "Support>0",
  background_filter = NULL,
  fg_sample_size = NULL,
  bg_sample_size = NULL,
  verbose = TRUE
)

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).

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_iterate_overlap(), XGR_merge_and_process(), XGR_parse_metadata(), XGR_plot_enrichment(), XGR_query(), XGR_sep_handler(), xgr_example

Examples

## Not run: 
fg_bg <- echoannot:::XGR_prepare_foreground_background(
    dat = echodata::get_Nalls2019_merged(),
    foreground_filter = "Consensus_SNP==TRUE",
    background_filter = "leadSNP==TRUE"
)

## End(Not run)

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