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 Farrall (2005); the random-effects model is described in Nicodemus (submitted) and saves a text file to the current working directory of all results printed to screen (use getwd() to find cwd).

Usage

catmapobject<-catmap(dataset, ci, printout, print.all) 

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). The dataset argument to catmap should be either the example data or a file containing the data for catmap, not an R object.
ci The confidence level for confidence intervals; 0 < ci < 1. The default is 0.95
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. Default = TRUE.
print.all Logical. Should individual-study ORs, CIs and weights be printed to screen and appended to dataset.output.txt? Default = FALSE.

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 Farrall (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). If users request a file to be created containing the results the file will be saved to the current working directory, which users can find by using >getwd(). Note that a catmap object must be created on the first call to catmap. If you do not create a catmap object you will not be able to use any of the other functions AND you will get a printout of the entire contents to screen

Author(s)

Kristin K. Nicodemus, kristin.nicodemus@well.ox.ac.uk

See Also

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

Examples

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

[Package catmap version 1.5 Index]