Package 'snplist'

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

Package:	snplist
Type:	Package
Version:	0.18.1
Date:	2017-12-11
License:	GPL-3

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 <[email protected]>

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

geneSets	An object created by the makeGeneSet() function.
fname	The name of the PLINK file to be created.

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

genes	A vector of gene names matching hgnc_symbol in the Ensembl database.
verbose	A Boolean indicating whether to output the funcitons progress in terms of the dimensions of the data.frame being constructed. Default is FALSE.
...	Additional arguments passed on to the internal call to biomaRt::useMart(...). If no such arguments are provided, useMart("ensembl", dataset="hsapiens_gene_ensembl") is run by default.

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

annoInfo	A vector of rsIDs, a data.frame with an 'rsid' column, or a file with one rsID per line. The SNP sets will be restricted to contain only the SNPs listed here. Default is NULL, in which case all SNPs present in the SNP table in the SQLite database will be used.
margin	A number, indicating the size of the neighborhood (in base pairs) surrounding a genes start and end positions in which a SNP will be included in that genes SNP set. Default is 0.
annoTable	A string indicating the name of the SQLite table for the rsIDs from annoInfo. Also used in naming the resulting table of SNP sets ('<name>ToGene'). Default is 'anno'.
geneTable	Name of the SQLite table containg chromosome, start and end positions for each gene, as previously created by setGeneTable. Default is 'gene'.
allTable	Name of the SQLite table containg chromosome and position for each SNP, as previously created by setSNPTable. Default is 'allchrpos'.
db	Name of the SQLite database in which to find the gene and SNP tables and create the SNP set table. Default is 'snplistdb'.
dbCleanUp	Boolean indicating if the tables and views created by the function should be dropped after the SNP set is returned. Default is FALSE.

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:

<gene name>

Vector of rsIDs of SNPs within <gene> (or the neighborhood around it)

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

geneInfo	A data.frame object of gene location info with columns 'gene','chr','start', and 'end'.
table	Name of the SQLite table to be created. Default is 'gene'.
db	Name of the SQLite database in which to create table. Default is 'snplistdb'.

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

snpInfo	A data.frame object of SNP location info with columns 'chr','pos', and 'rsid', or a tab-delimited file with those columns and one record per row.
table	Name of the SQLite table to be created. Default is 'allchrpos'.
db	Name of the SQLite database in which to create table. Default is 'snplistdb'.

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)

---