My apologies, what I had in mind was obtaining the full snp sequence, similar to how we obtain a proteins sequence.
mart <- useMart(host="www.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
ENSG <- getBM(mart=mart, attributes="ensembl_gene_id", filters="hgnc_symbol", values="CTNS")
# The two lines above work ok, we setup "mart" to look at human genes and ENSG to contain the ensembl id for "CTNS" gene which is involved in the disease of interest. The line below setups "snpmart" to point to the snp database.
snpmart <- useMart(host="www.ensembl.org", biomart="ENSEMBL_MART_SNP", dataset="hsapiens_snp")
# The line below is where I get totally lost.
seq1 = getSequence(id="CTNS",type="entrezgene",seqType="cdna", mart=snpmart)
# It maybe that you cant get cdna sequences from snp database. However, I have had a bit luck by modifying some code written by Steffen...
getBM(attributes=c("refsnp_id","snp"),filters=c("snp_filter","downstream_flank","upstream_flank"),values=list(snp[1:5,1],20,20),mart=snpmart, checkFilters=FALSE)
This allows a predefined length of cdna to be extracted around the snp. I'm not sure what filters and attributes to use to figure out how big each snp is and thus get the entire sequence.
It would help if you said exactly what you are looking for. Unfortunately 'the full sequence of SNP data' and 'full cdna associated with a gene (and SNP)' is rather inexact. What would the output you desire look like?