COLOC_merge_res: Prepare data for coloc plot

In RajLabMSSM/catalogueR: QTL data extraction and colocalization

Prepare data for coloc plot

Description

Use the coloc results (coloc_QTLs) to determine which full summary stats (gwas.qtl_paths) to plot.

Usage

COLOC_merge_res(
  gwas.qtl_paths,
  coloc_QTLs = NULL,
  qtl_thresh = 1e-05,
  coloc_thresh = 0.8,
  gwas_label = "GWAS",
  remove_extra_panes = TRUE,
  verbose = TRUE
)

Arguments

gwas.qtl_paths	Query results paths from eQTLcatalogue_query.
coloc_QTLs	Colocalization results from COLOC_run.
qtl_thresh	QTL uncorrected p-value ("pvalues.QTL") threshold.
coloc_thresh	Colocalization Posterior Probability threshold, using the formula: (PP.H3 + PP.H4 >= coloc_thresh) & (PP.H4 / PP.H3 >= 2.
gwas_label	Label for the GWAS subplot.
remove_extra_panes	Remove SNPs from non-significant panes.
verbose	Print messages.

See Also

Other coloc: COLOC_corplot(), COLOC_get_example_res(), COLOC_get_res(), COLOC_heatmap(), COLOC_report_summary(), COLOC_run()

RajLabMSSM/catalogueR documentation built on Jan. 1, 2023, 10:45 a.m.