Case-Control and TDT Meta-Analysis Package

Although many software tools can perform meta-analyses on genetic case-control data, none of these apply to combined case-control and family-based (TDT) studies. This package conducts fixed-effects (with inverse variance weighting) and random-effects [DerSimonian and Laird (1986) ] meta-analyses on combined genetic data. Specifically, this package implements a fixed-effects model [Kazeem and Farrall (2005) ] and a random-effects model [Nicodemus (2008) ] for combined studies.


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
## 1  Peter,2002     2  0  0      316         338         220            218
## 2 Abrams,2001     2  0  0      710         146         422             96
## 3   Todd,2003     2  0  0     1004         344         233            543
## 4     Yu,2007     2  0  0     3344         434         544            322
## 5    Wei,2007     1 65 32        0           0           0              0

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

News

catmap 1.6.4


  • Modified visualization tools
    • Moved "Weight (%)" column to end of figure
    • Added summary diamond and weights to all figures
    • Slight change to appearance of confidence intervals
    • Slight change to how studies get named

catmap 1.6.3


  • Modified makeForest
    • Use grid to call grid.newpage() before plotting
    • Study weights added to summary forest plots
    • Dashed line added to summary forest plots

catmap 1.6.2


  • Add unit tests for core functions
    • test_catmap.R unit tests complete and validated
    • test_forest.R unit tests complete and validated
  • Major revisions to catmap.funnel
    • Function now rebuilt using metafor package
  • Major revisions to forest plots
    • New makeForest function builds all forest figures
    • Modified catmap.forest to use makeForest
    • Modified catmap.cumulative to use makeForest
    • Modified catmap.sense to use makeForest

catmap 1.6.1


  • Major revisions to global package architecture
    • Convert Rd files to Roxygen format
    • Add DOIs to package DESCRIPTION
    • Add NEWS and README files
  • Major revisions to catmap function
    • Function now takes data.frame or matrix input
    • Function now returns output as a list object
    • Removed redundant and superfluous code
    • Removed print.all argument entirely
    • Revised documentation
  • Major revisions to catmapdata data
    • Store catmapdata object in RDA format
    • Fix WARNING associated with catmapdata manual
    • Revised documentation

Reference manual

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install.packages("catmap")

1.6.4 by Thomas Quinn, 2 years ago


http://github.com/tpq/catmap


Report a bug at http://github.com/tpq/catmap/issues


Browse source code at https://github.com/cran/catmap


Authors: Thomas Quinn [aut, cre] , Kristin Nicodemus [aut] , Glaucia Martins [ctb] , Carlos Maia [ctb]


Documentation:   PDF Manual  


GPL-2 license


Imports forestplot, grid, metafor

Depends on stats

Suggests knitr, testthat


See at CRAN