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

Please see the example function calls below, or refer to the individual function documentation or the included vignette for more information.

Author(s)

Authors: Chanhee Yi, Alexander Sibley, and Kouros Owzar Maintainer: Alexander Sibley <alexander.sibley@dm.duke.edu>

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)

## Not run: 
setGeneTable(geneInfo)
setSNPTable(snpInfo)
geneset <- makeGeneSet(annoInfo)
exportPLINKSet(geneset,"geneSet.set")
file.show("geneSet.set")

## End(Not run)

exportPLINKSet

Description

Simple function using Rcpp to write the gene set to a file in the PLINK set format.

Usage

  exportPLINKSet(geneSets, fname)	

Arguments

Value

A Boolean indicating if the file was successfully written.

See Also

makeGeneSet

Examples

    # Please see the vignette or the package description 
    # for an example of using this function.

getBioMartData

Description

A function leveraging the biomaRt package to retrieve gene chromosome and start and end positions from Ensembl.

Usage

    getBioMartData(genes,verbose=FALSE,...) 

Arguments

Value

A data.frame object with columns 'gene','chr','start', and 'end', suitable for input to the setGeneTable function.

Note

At the time of package release, the BioMart community portal is temporarily unavailable. See www.biomart.org for updated status or more information. To access alternative hosts, pass additional arguments to the internal call to biomaRt::useMart(...), as in the second example below.

References

Durinck S., Spellman P.T., Birney E. and Huber W. (2009) Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt, Nature Protocols, 4, 1184–1191.

See Also

setGeneTable

Examples

## Not run: 
getBioMartData(c("BRCA1","BRCA2"))
getBioMartData(c("BRCA1","BRCA2"), 
               host="www.ensembl.org", 
               biomart="ENSEMBL_MART_ENSEMBL", 
               dataset="hsapiens_gene_ensembl")

## End(Not run)

makeGeneSet

Description

This function uses existing SQLite tables (from setGeneTable and setSNPTable) to make SNP sets. The SNP Set for each gene is the collection of SNPs located either between the start and end locations of the gene, or within a specified neighborhood around the gene. The SNP Sets are stored in the SQLite database, and returned as a list object.

Usage

    makeGeneSet(annoInfo=NULL,margin=0,annoTable='anno',geneTable='gene',
                        allTable='allchrpos',db='snplistdb',dbCleanUp=FALSE)

Arguments

Details

Note: This function relies on the prior execution of the setGeneTable and setSNPTable functions and the SQLite databes and tables they create. If the table or db argument in either of those functions is changed from the default value, it must also be changed here.

Value

Returns a list of SNP sets of the form:

See Also

setGeneTable, setSNPTable, snplist-package

Examples

    # Please see the vignette or the package description 
    # for an example of using this function.

setGeneTable

Description

Takes a data.frame object with columns 'gene','chr','start', and 'end', and creates an SQLite table of the information. Returns a count of the number of genes in the table.

Usage

    setGeneTable(geneInfo,table='gene',db='snplistdb') 

Arguments

Value

Count of genes included in table.

Examples

    geneInfo <- cbind(c('BRCA1','BRCA2'),c(17,13),c(41196312,32889611),c(41277500,32973805))
    colnames(geneInfo) <- c('gene','chr','start','end')
    ## Not run: 
    setGeneTable(as.data.frame(geneInfo))
    
## End(Not run)

setSNPTable

Description

Takes a file or data.frame object with columns 'chr','pos', and 'rsid', and creates an SQLite table of the information. Returns a count of the number of SNPs in the table.

Usage

    setSNPTable(snpInfo,table='allchrpos',db='snplistdb')

Arguments

Value

Count of genes included in table.

Examples

    snpInfo <- cbind(c(17,17,13,13),
		     c(41211653, 41213996, 32890026,32890572),
		     c("rs8176273","rs8176265","rs9562605","rs1799943") )
    colnames(snpInfo) <- c('chr','pos','rsid')
    ## Not run: 
    setSNPTable(as.data.frame(snpInfo))
    
## End(Not run)