In tpq/catmap: Case-Control and TDT Meta-Analysis Package

Introduction

This package conducts fixed-effects (with inverse variance weighting) and random-effects (DerSimonian and Laird (1986)) meta-analyses of case-control or family-based (TDT) genetic data. In addition, catmap performs meta-analyses which combine these two types of study designs. Specifically, this package implements a fixed-effects model (Kazeem and Farrall (2005)) and a random-effects model (Nicodemus (2008)) for combined studies. This package was removed from the CRAN repository sometime after 2009. This is a rendition of the original package updated to work with the newest version of R. The algorithms have not changed since catmap version 1.6.0; however, this version has added some aesthetic improvements.

Quick start

The main function, catmap, accepts data.frame, matrix, or file input. See ?catmapdata for help.

library(catmap)
data(catmapdata)
catmapdata

It is important to save the output of the catmap function for the next step in the analysis.

c1 <- catmap(catmapdata, 0.95, FALSE)

Four secondary functions use the output of the catmap function to build the meta-analysis figures, including the forest plot and the funnel plot. The functions below output these figures to the working directory as pdf files.

# Make forest plots
?catmap.forest
?catmap.sense
?catmap.cumulative

# Make funnel plot
?catmap.funnel

tpq/catmap documentation built on May 31, 2019, 6:49 p.m.