plot_dataset_overlap: Plot inter-study SNP overlap

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

Plot inter-study SNP overlap

Description

Cross-tabulate SNP overlap (after applying filter) between each pair of studies.

Usage

plot_dataset_overlap(
  merged_DT,
  snp_filter = "!is.na(SNP)",
  filename = NA,
  formula_str = "~ SNP + Dataset",
  triangle = FALSE
)

Arguments

merged_DT	Merged fine-mapping results data from finemap_loci.
snp_filter	Filter to use apply to SNPs before plotting.
filename	Path to save file to as PNG.
formula_str	Formula passed to xtabs.
triangle	Plot correlation matrix as a square or a triangle.

See Also

Other summarise: CS_bin_plot(), CS_counts_plot(), peak_overlap_plot(), super_summary_plot()

Examples

## Not run: 
    merged_DT <- echodata::get_Nalls2019_merged()
    merged_DT$Dataset <- rep(c("Dataset1","Dataset2"),nrow(merged_DT)/2)
    snp_xprod <- plot_dataset_overlap(merged_DT = merged_DT)
    

## End(Not run)

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