gwas: GWAS summary
In tobyjohnson/gtx: Genetics ToolboX

Description Usage Arguments Details Value Author(s)

Summarize and visualise GWAS results.

gwas(analysis,
     style = c('manhattan', 'qqplot'), 
     pval_thresh = 5e-08, maf_ge, rsq_ge,
     gene_annotate = TRUE,
     plot_ymax = 30,
     manhattan_thresh = 5e-08,
     manhattan_col = c('#064F7C', '#6D97BD'),
     manhattan_interspace = 50e6,
     qqplot_col = '#064F7C',
     qqplot_alpha = 0.01,
     plot_fastbox = 2, 
     dbc = getOption("gtx.dbConnection", NULL))

`analysis`	The key value for the GWAS analysis to summarize
`style`	Character vector specifying plot style(s)
`pval_thresh`	P-value threshold for top hits table
`maf_ge`	MAF greater-or-equal threshold
`rsq_ge`	Imputation r-squared greater-or-equal threshold
`gene_annotate`	Logical, whether to annotate top hits with gene names
`plot_ymax`	Y axis maximum, -log10(p) scale, for plots
`manhattan_thresh`	P-value for threshold line on Manhattan plot
`manhattan_col`	Chromosome colour cycle for Manhattan plot
`manhattan_interspace`	Chromosome interspacing for Manhattan plot
`qqplot_col`	Colour for QQ plot
`qqplot_alpha`	Null envelope alpha value for QQ plot
`plot_fastbox`	Box height for fast approximate plotting
`dbc`	Database connection

This high level function summarizes and visualizes results (i.e. complete summary statistics) from a single GWAS analysis.

Currently, a distance-pruned table of top hits, and optional Manhattan and QQ plots, are generated.

The distance pruning and gene annotation is currently very slow and needs to be optimized.

The Manhattan and QQ plots use an approximation to speed up both the data query and the plot rendering, where boxes or lines are drawn instead of individual points, for y-axis values between 0 and plot_fastbox. Faint grey hatching is shown over this part of the plot to indicate that the true data are not being plotted.

Y-axis points are truncated, but this needs to be made more clear in the plot.

gwas returns a data frame containing the distance pruned top hits.

Toby Johnson Toby.x.Johnson@gsk.com

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.