[BioC] Output IUPAC genotypes from oligo?

[Benilton Carvalho]

Dear Hollis,

if your dataset is comprised of samples on the SNP 6.0 chip, I'd
strongly recommend you to use the 'crlmm' package to get the genotype
calls. The algorithm in that package has the improvements described in
[1]. However, it'll still give you calls in the 1/2/3 format.

Currently, there are no tools to give you calls in the IUPAC code. You
could do this 'manually' by comparing the results you get against a
table having the SNP ID, allele A, allele B and strand info, which you
can obtain with:

library(pd.genomewidesnp.6)
conn = db(pd.genomewidesnp.6)
sql = 'SELECT man_fsetid, allele_a, allele_b, strand FROM featureSet'
snpInfo = dbGetQuery(conn, sql)

On the 'snpInfo' table, please note that 0 stands for sense and 1
stands for antisense strand.

HTH,
benilton


[1] Carvalho BS, Louis TA, Irizarry RA. Quantifying uncertainty in
genotype calls. Bioinformatics. 2010 Jan 15;26(2):242-9. Epub 2009 Nov
11. PMID: 19906825


On 25 April 2011 21:34, Hollis Wright <wrighth at ohsu.edu> wrote:
> Hello, all; searched but did not find a solution to this. I have some 6.0 arrays that I've normalized and done calls for with as per the oligo vignette. However, the calls are still in the 1/2/3 format and I'd like to get them into (preferably) an IUPAC code for the actual forward strand nucleotide. Is there an easy way to do this?
>
> Hollis Wright, PhD
> Knight Cancer Center
> Oregon Health and Science University
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