catmap {catmap}R Documentation

catmap: Case-control And TDT Meta-Analysis Package

Description

catmap is an R package that conducts fixed-effects (inverse variance) and random-effects (DerSimonian and Laird, 1986) meta-analyses of case-control or family-based (TDT) genetic data; in addition, it performs meta-analyses combining these two types of study designs. The fixed-effects model was first described by Kazeem and Farrell (2005); the random-effects model is described in Nicodemus (submitted).

Usage

catmapobject<-catmap(dataset, ci, printout) 

Arguments

dataset A text file containing a header with the following column names: name, study, t, nt, caserisk, controlrisk, casenotrisk, controlnotrisk in tab-delimited format. Note that the header must be exactly as specified and that all cells in the table must have an entry, even if the entry is 0 or missing (NA). See for example: data(catmapdata).
ci The confidence level for confidence intervals; 0 < ci < 1
printout Logical. Should a text file of the fixed- and random-effects models and Q statistic results be saved to the current working directory? Output files are saved with the default name of dataset.output.txt where dataset is the name of the file given as the first argument to catmap.

Details

catmap is an R package that conducts fixed-effects (inverse variance) and random-effects (DerSimonian and Laird, 1986) meta-analyses of case-control or family-based (TDT) genetic data; in addition, it performs meta-analyses combining these two types of study designs. The fixed-effects model was first described by Kazeem and Farrell (2005); the random-effects model is described in Nicodemus (submitted). Cumulative meta-analyses over time and leave-one-out sensitivity analyses may be performed using either fixed- or random-effects estimates or both estimates may be calculated; both produce a .txt file and an optional .pdf plot as output. A funnel plot graphic is implemented; however, no formal test of publication bias is available (see Ioannidis & Trikalinos, 2007). Note that a catmap object must be created on the first call to catmap.

Author(s)

Kristin K. Nicodemus, nicodemusk@mail.nih.gov or knicodem@jhsph.edu

See Also

catmap.forest, catmap.sense, catmap.cumulative, catmap.funnel.

Examples

## Not run: 
data(catmapdata)        
catmap(catmapdata, 0.95, TRUE)
catmapobject1<-catmap(catmapdata, 0.95, TRUE)
## End(Not run)

[Package catmap version 1.2 Index]