snplist (version 0.13)

snplist-package: Tools to create Gene Sets

Description

A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example for use with the RSNPset package, or to export to a PLINK set.

Details

ll{ Package: snplist Type: Package Version: 0.13 Date: 2014-12-03 License: GPL-3 } Please see the example function calls below, or refer to the individual function documentation or the included vignette for more information.

See Also

RSQLite, Rcpp

Examples

chromosome <- c(1,5,22,"X","Y","MT")

geneNum <- 5
snpNum <- 1200
annoDataNum <- 500

chrLength <- 1000
geneLength <- 100

gene <- paste("gene",1:geneNum,sep="")
chr <- sample(chromosome,geneNum,replace=TRUE)
start <- sample(chrLength,geneNum,replace=TRUE)
d <- sample(geneLength,geneNum,replace=TRUE)
end <- start+d
geneInfo <- data.frame(gene,chr,start,end)

rsid <- paste("rs",1:snpNum,sep="")
chr <- sample(chromosome,snpNum,replace=TRUE)
pos <- sample(chrLength+geneLength,snpNum,replace=TRUE)
snpInfo <- data.frame(rsid,chr,pos)

annoInfo <- data.frame("rsid"=sample(rsid,annoDataNum))

dim(geneInfo)
dim(snpInfo)
dim(annoInfo)

setGeneTable(geneInfo)
setSNPTable(snpInfo)
geneset <- makeGeneSet(annoInfo)
exportPLINKSet(geneset,"geneSet.set")
file.show("geneSet.set")