FitGMLD: estimate a graphical model for linkage disequilibrium

In rJPSGCS: R-Interface to Gene Drop Simulation from JPSGCS

Description

This function is an R wrapper for the JPSGCS program to estimate a graphical model for linkage disequilibrium (LD) from a sample of genotypes. The genetic markers are assumed to be on the same chromosome.

Usage

FitGMLD(par = "input.par", fped = "flipped.ped", out.ld.par = "out.ld.par")

Arguments

par	Name of a LINKAGE parameter file (also called a DATAFILE: see http://linkage.rockefeller.edu/soft/linkage/) that contains marker and genetic map information.
fped	Name of a LINKAGE pedigree file “flipped” so that rows correspond to loci and columns correspond to individuals.
out.ld.par	Name of the file in the current working directory to contain the fitted LD model.

Details

The input pedigree file fped is not the standard format where rows correspond to individuals and columns to loci. Rather, it has been transposed so that rows correspond to loci. Transposed LINKAGE pedigree files may be written by the write.pedfile function with the option transpose=TRUE.

Further information on the graphical model is available from the article listed in the References.

Value

None. The result of the function call is the output file out.ld.par.

Note

This function can require large amounts of memory for large data sets (e.g. whole chromosomes of SNPs at the marker density of the HapMap project). The computation for fitting the LD model is done in java, using functions from Alun Thomas' suite of Java Programs for Statistical Genetics and Computational Statistics (JPSGCS). The JPSGCS java programs are accessed by R-wrappers provided by the rJPSGCS package, which initializes the java virtual machine (JVM) if not already done so by another package. To over-ride the default amount of memory java allocates for heap space, initialize the JVM before loading rJPSGCS as follows:

   options(java.parameters="-Xmx2048m") #set max heap space to 2GB
   library(rJava)
   .jinit() #initialize the JVM
   library(rJPSGCS) # now load rJPSGCS
   

Author(s)

Sigal Blay, Jinko Graham and Brad McNeney

References

Thomas A. Estimation of graphical models whose conditional independence graphs are interval graphs and its application to modeling linkage disequilibrium. Comput Stat Data Anal. 2009; 53:1818-1828.

See Also

write.parfile, write.pedfile

Examples

## Not run: 
data(exdat)
sdat<-as(exdat$markers,"snp.matrix") #coerce to snp.matrix
# Write a LINKAGE parameter file 
write.parfile(snp.data=sdat,map=exdat$map,file="test.par")
# Write a "flipped" pedfile for the SNP data on unrelated subjects.
write.pedfile(pedinf="unrelated",snp.data=sdat,file="ftest.ped",transpose=TRUE)
FitGMLD(par="test.par",fped="ftest.ped",out.ld.par="test.ld.par")
# Clean up
unlink(c("test.par","ftest.ped","test.ld.par"))

## End(Not run)

rJPSGCS documentation built on May 1, 2019, 11:10 p.m.