geneInfo {RSNPper}R Documentation

use CHIP SNPper XML-RPC service to extract gene or SNP information

Description

SNPper is a web service at chip.org (see Riva and Kohane, Bioinformatics 2002). This function sets up the XML RPC call for the GENEINFO service.

Usage

geneInfo(name=NA, acc=NA, id=NA)
SNPinfo(dbsnpid=NA)
geneLayout(id=NA)
geneSNPs(id=NA, acc=NA)
itemsInRange(item="genes", chr, start, end)
useSNPper(cmd, parmstring)
useSNPper2(cmd, parmstring)

Arguments

name name: standard gene name
acc acc: mrna accession number
id id: SNPper gene id. This is a 'private' nomenclature, to find the value for a given gene, use geneInfo.
dbsnpid dbsnpid: numeric value after 'rs' in dbSNP id
item item: string, either "genes", "snps", or "countsnps"
cmd cmd: character string identifying an XML-RPC call honored by SNPPER; see list .rpcCalls in package
parmstring parmstring: character string supplying parm=value information
chr chr: string beginning with 'chr' identifying chromosome of interest
start start: start in base pair count of region of interest; use a string to avoid problems with scientific notation
end end: end in base pair count of region of interest; use a string to avoid problems with scientific notation

Details

runs an xmlEventParse on the XML-RPC response and packages the results.

Value

an attributed, named character vector. The attribute gives version info for the SNPper database build.

Note

The itemsInRange function with item argument 'countsnps' is a hack that does not use XML parsing because the countsnps XML-RPC returns illegitimate XML tags. Thus there is no toolInfo attribute for this specific call. All other functions return textual information coupled with a 'toolInfo' attribute which details the SNPper database version, the golden path build version, and the dbSNP database version from which the SNPper resources were constructed.

NB: A revised version of the XML package now allows direct parsing of R connection streams. This will be employed ASAP, once the necessary general XML infrastructure becomes prevalent.

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

References

Riva A and Kohane IS, SNPper: retrieval and analysis of human SNPs, Bioinformatics 18(12) 2002, pp1681-1685.

Examples

if (interactive())
 {
 print(geneInfo("CRP"))
 print(geneLayout("546"))
 tmp <- geneSNPs("546")
 print(length(tmp))
 glist <- itemsInRange("genes","chr1", "155000000", "157000000")
 print(SNPinfo("25"))
 print(length(glist))
 print(itemsInRange("countsnps","chr1", "156000000", "157000000"))
 print(useSNPper("geneinfo","&name=CRP"))
 }

[Package RSNPper version 1.0-2 Index]