[BioC] pulling functional information for SNPs

[James W. MacDonald]

Hi Seth,

Seth Falcon wrote:
> Hi Jim,
> 
> On 5/4/10 11:56 AM, James W. MacDonald wrote:
>> Getting a query for 700K things will likely take a long time. Had you
>> mentioned that you were using the Affy 6.0 chip, we could have gone in a
>> different direction.
>>
>> biocLite("pd.genomewidesnp.6") ## this will take a while
>> library(pd.genomewidesnp.6)
>> con <- pd.genomewidesnp.6 at getdb()
>> ## there might be a better way of setting up the connection...
>> ## If so, Benilton will correct me very soon ;-P
>>
>> ## check things out
>>  > dbListTables(con)
>> [1] "featureSet" "featureSetCNV" "pmfeature" "pmfeatureCNV"
>> [5] "sequence" "sequenceCNV" "sqlite_stat1" "table_info"
>>  > dbListFields(con, "featureSet")
>> [1] "fsetid" "man_fsetid" "affy_snp_id" "dbsnp_rs_id"
>> [5] "chrom" "physical_pos" "strand" "cytoband"
>> [9] "allele_a" "allele_b" "gene_assoc" "fragment_length"
>> [13] "fragment_length2" "dbsnp" "cnv"
>>
>> ## try a 70K query - I won't show how I made the snp vector...
>>
>>  > length(snps)
>> [1] 70000
>>  > system.time(dbGetQuery(con, paste("select dbsnp_rs_id, chrom,
>> physical_pos from featureSet where dbsnp_rs_id in ('", paste(snps,
>> collapse = "','"), "');", sep = "")))
>> user system elapsed
>> 4.89 1.09 119.09
>>
>> So about 2 min for 70K query. Not bad.
> 
> I was curious about this and tried the above on my laptop, a MacBook Pro 
> running at 2.53GHz 4GB RAM (pretty sure it has a 5400 rpm disk)  I get a 
> result for the above in ~4 sec.  And I can retrieve 800K in ~30 sec.
> 
> Did you use a particularly slow system (NFS perhaps?)

Well, the hard drive isn't that slow - it's a 7200 rpm Seagate 
Barracuda. However, the comp is a Pentium 4 (3GHz) with 1 Gb RAM. I'm 
sort of shocked that this sled of a computer is that bad though...

Jim


> 
> + seth
> 
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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