gap: METAL_forestplot – R documentation

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METAL_forestplot

forest plot as R/meta's forest for METAL outputs

Description

This functions takes a meta-data from METAL (tbl) and data from contributing studies (all) for forest plot. It also takes a SNPID-rsid mapping (rsid) as contributing studies often involve discrepancies in rsid so it is appropriate to use SNPID, i.e., chr:pos_A1_A2 (A1<=A2).

Usage

METAL_forestplot(tbl,all,rsid,package="meta",...)

Arguments

`tbl`	Meta-anslysis summary statistics
`all`	statistics from all contributing studies
`rsid`	SNPID-rsid mapping file
`package`	style of plot as in meta, rmeta or forestplot
`...`	options to use for the pdf device

Details

The study-specific and total sample sizes (N) can be customised from METAL commands

CUSTOMVARIABLE N
LABEL N as N
WEIGHTLABEL N

Value

It will generate a forest plot specified by pdf for direction-adjusted effect sizes.

References

Scharzer G. (2007). meta: An R package for meta-analysis. R News, 7:40-5, https://cran.r-project.org/doc/Rnews/Rnews_2007-3.pdf, https://CRAN.R-project.org/package=meta.

Willer CJ, Li Y, Abecasis GR. (2010). METAL: fast and efficient meta-analysis of genomewideassociation scans. Bioinformations. 26:2190-1, https://github.com/statgen/METAL, https://genome.sph.umich.edu/wiki/METAL.

Author(s)

Jing Hua Zhao

Examples

## Not run: 
require(gap.datasets)
data(OPG)
METAL_forestplot(OPGtbl,OPGall,OPGrsid,width=8.75,height=5)

## End(Not run)

gap

Genetic Analysis Package

v1.2.3-1

GPL (>= 2)

Authors

Jing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley

Initial release

2021-4-21