COLOC_plot_loci: Faceted Manhattan plots of QTL datasets

In RajLabMSSM/catalogueR: QTL data extraction and colocalization

Faceted Manhattan plots of QTL datasets

Description

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

Usage

COLOC_plot_loci(
  gwas.qtl_paths = NULL,
  coloc_QTLs = NULL,
  plot_dat = NULL,
  qtl_thresh = 1e-05,
  coloc_thresh = 0.8,
  gwas_label = "GWAS",
  remove_extra_panes = TRUE,
  y_facet_angle = 0,
  x_facet_angle = 270,
  show_plot = TRUE,
  verbose = TRUE
)

Arguments

gwas.qtl_paths	Query results paths from eQTLcatalogue_query.
coloc_QTLs	Colocalization results from COLOC_run.
plot_dat	[Optional] Pre-computed plot data from COLOC_merge_res.
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.
y_facet_angle	Angle of the y-axis facet labels.
x_facet_angle	Angle of the x-axis facet labels.
show_plot	Whether to print the plot.
verbose	Print messages.

Examples

coloc_QTLs <- catalogueR::COLOC_get_example_res()
gwas.qtl_paths <- catalogueR::eQTLcatalogue_example_queries()
gg_gwas.qtl <- catalogueR::COLOC_plot_loci(
    gwas.qtl_paths = gwas.qtl_paths,
    coloc_QTLs = coloc_QTLs,
    coloc_thresh = .5,
    qtl_thresh = .005,
    remove_extra_panes = FALSE)  

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