P-Z plot

P-Z plot

pzPlot(x, beta_column = "Est", se_column = "Est.SE", pval_column = "p.value")

Arguments

x

data.frame / list of data.frames (output of ds.GWAS) Single table of results or list of tables (default output of ds.GWAS).

beta_column

character (default "Est") Name of the column containing the betas.

se_column

character (default "Est.SE") Name of the column containing the SE.

pval_column

character (default "p.value") Name of the column containing the p-values.

Value

A ggplot object

Details

Plot to reveal issues with beta estimates, standard errors and P values. The plots compare P values reported in the association GWAS with P values calculated from Z-statistics (P.ztest) derived from the reported beta and standard error. A study with no issues should show perfect concordance. It will generate a plot per study, where concordance of all the study SNPs will be displayed.