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

Usage

METAL_forestplot(
  tbl,
  all,
  rsid,
  flag = "",
  package = "meta",
  method = "REML",
  split = FALSE,
  ...
)

Arguments

tbl: Meta-anslysis summary statistics.
all: statistics from all contributing studies.
rsid: SNPID-rsid mapping file.
flag: a variable in tbl such as cis/trans type.
package: "meta" or "metafor" package.
method: an explcit flag for fixed/random effects model.
split: when TRUE, individual prot-MarkerName.pdf will be generated.
...: Additional arguments to meta::forest or metafor::forest.

Value

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

Details

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).

The study-specific and total sample sizes (N) can be customised from METAL commands. By default, the input triplets each contain a MarkerName variable which is the unique SNP identifier (e.g., chr:pos:a1:a2) and the tbl argument has variables A1 and A2 as produced by METAL while the all argument has EFFECT_ALLELE and REFERENCE_ALLELE as with a study variable indicating study name. Another variable common the tbl and all is prot variable as the function was developed in a protein based meta-analysis. As noted above, the documentation example also has variable N. From these all information is in place for generation of a list of forest plots through a batch run.

CUSTOMVARIABLE N
LABEL N as N
WEIGHTLABEL N

References

Schwarzer G (2007). “meta: An R package for meta-analysis.” R News, 7, 40-45. https://cran.r-project.org/doc/Rnews/Rnews_2007-3.pdf. Willer CJ, Li Y, Abecasis GR (2010). “METAL: fast and efficient meta-analysis of genomewide association scans.” Bioinformatics, 26(17), 2190-1. doi:10.1093/bioinformatics/btq340 .

Author

Jing Hua Zhao

Examples

if (FALSE) { # \dontrun{
 data(OPG, package="gap.datasets")
 meta::settings.meta(method.tau="DL")
 METAL_forestplot(OPGtbl,OPGall,OPGrsid,width=8.75,height=5,digits.TE=2,digits.se=2,
                  col.diamond="black",col.inside="black",col.square="black")
 METAL_forestplot(OPGtbl,OPGall,OPGrsid,package="metafor",method="FE",xlab="Effect",
                  showweights=TRUE)
} # }