snplist.R
In snplist: Tools to Create Gene Sets

## ----setup1, include=FALSE----------------------------------------------------
require(knitr)
opts_chunk$set(fig.path='figure/beamer-',fig.align='center',fig.show='hold',size='footnotesize')

## ----setup2, include=FALSE------------------------------------------
options(width=70)  # make the printing fit on the page
set.seed(1121)     # make the results repeatable
stdt<-date()

## ----genes----------------------------------------------------------
genes <- c("BRCA1","BRCA2")

## ----snps-----------------------------------------------------------
snpInfo <- data.frame(chr=c(17,17,13,13),
                      pos=c(41211653,41213996,32890026,32890572),
                      rsid=c("rs8176273","rs8176265","rs9562605","rs1799943"),
                      stringsAsFactors=FALSE)

## ----loadpkg--------------------------------------------------------
library(snplist)

## ----biomart1, eval=FALSE-------------------------------------------
#  geneInfo <- getBioMartData(genes, biomart="ENSEMBL_MART_ENSEMBL",
#                                       host="grch37.ensembl.org",
#                                       path="/biomart/martservice",
#                                    dataset="hsapiens_gene_ensembl")

## ----biomart2, include=FALSE----------------------------------------
geneInfo <- data.frame(gene=c("BRCA1","BRCA2"),
                      chr=c(17,13),
                      start=c(41196312, 32889611),
                      end=c(41277500, 32973805),
                      stringsAsFactors=FALSE)

## ----biomart3-------------------------------------------------------
geneInfo

## ----genetbl--------------------------------------------------------
setGeneTable(geneInfo) 

## ----snptbl---------------------------------------------------------
setSNPTable(snpInfo)

## ----snpset1, size='tiny'-------------------------------------------
geneset <- makeGeneSet(margin=50000) 

## ----snpset2, tidy=FALSE, size='tiny'-------------------------------
chipSNPs <- c("rs0000000","rs8176273","rs9562605")
geneset2 <- makeGeneSet(annoInfo=chipSNPs, 
			annoTable='myChip') 

## ----plink----------------------------------------------------------
exportPLINKSet(geneset2, "mySNPset.set") 

## ----sesinf, echo=FALSE, results="asis"-----------------------------
toLatex(sessionInfo(), locale=FALSE)

## ----times, echo=FALSE----------------------------------------------
print(paste("Start Time",stdt))
print(paste("End Time  ",date()))

## ----cleanup, include=FALSE-----------------------------------------
file.remove("mySNPset.set") 
file.remove("geneSet.set") 
file.remove("snplistdb.sqlite")