gwas2: GWAS pairwise comparison

In tobyjohnson/gtx: Genetics ToolboX

Description

Compare results from two Genome Wide Association Studies.

Usage

gwas2(analysis1, analysis2, pval1_thresh = 5e-08, pval2_thresh = 5e-08,
  prune_dist = 500000L, dbc = getOption("gtx.dbConnection", NULL))

Arguments

analysis1	Analysis identifier for first GWAS (plot x-axis)
analysis2	Analysis identifier for second GWAS (plot y-axis)
pval1_thresh	Significance threshold for first GWAS. Default: 5e-08
pval2_thresh	Significance threshold for second GWAS. Default: 5e-08
prune_dist	Distance-based pruning threshold (for both). Default: 500000
dbc	Database connection. Default: getOption("gtx.dbConnection", NULL)

Details

Generates a plot showing (flipped) Z scores for all variants significant in either analysis. Distance-based pruning is applied separately to each analysis, and index variants for first/second/both analyses are shown as red/green/yellow down-triangles/up-triangles/squares. Using each set of index variants a GRS is constructed and tested for association in the other analysis.

Value

Invisible dataframe of significant variants, with prune1/2 columns added

Author(s)

Toby Johnson [e-mail]

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