pzPlot: P-Z plot
In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

pzPlot

R Documentation

P-Z plot

Description

P-Z plot

Usage

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.

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.