geneInfo {SNPtools} | R Documentation |
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.
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)
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 |
runs an xmlEventParse on the XML-RPC response and packages the results.
an attributed, named character vector. The attribute gives version info for the SNPper database build.
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.
Vince Carey <stvjc@channing.harvard.edu>
Riva A and Kohane IS, SNPper: retrieval and analysis of human SNPs, Bioinformatics 18(12) 2002, pp1681-1685.
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")) }