%\VignetteIndexEntry{snp location metadata overview}
%\VignetteKeywords{Genetical genomics,SNP,expression}
%\VignettePackage{GGBase}


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\begin{document}
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\title{A new approach to SNP location metadata}
\author{VJ Carey}
\maketitle

\section{Introduction}

Versions of GGtools prior to 2.3.x have a complicated approach
to SNP location metadata, involving a specially constructed
SQLite database.  %In the current version we will use a structure
%derived from the SNPlocs.Hsapiens.dbSNP.* package.
In versions of GGBase up to 3.11, some SNP location metadata
support was provided.  In GGBase 3.11 and beyond, users are responsible
for managing their own location metadata for SNPs and genes.  This
can be accomplished using the SNPlocs.Hsapiens.* package and other
annotation resources.  The GGtools cisProxScores function shows
some of the possibilities.

This vignette is retained as legacy for those who may want to retrieve
earlier versions of R/Bioconductor to employ formerly supported facilities.

One class and two methods are supported.

<<lkcl,eval=FALSE>>=
getClass("snpLocs")
data(hsSnpLocs)
hsSnpLocs
@

The chromosome-specific locations are generated reasonably
efficiently:
<<lkc,eval=FALSE>>=
snpLocs.Hs(chrnum(20), rsid("rs6060535"))
@

\section{Construction of serialized reference container}

First, unify the name and location information from the
SNPlocs package.

<<doco,eval=FALSE>>=
humanSNPlocs = list()
library(SNPlocs.Hsapiens.dbSNP.20071016)
if (file.exists("humanSNPlocs.rda")) 
  load("humanSNPlocs.rda") else {
  for (i in c(as.character(1:22), "X", "Y")) {
   curc = getSNPlocs(paste("chr", i, sep=""))
 rsid.int = as.integer(curc[,1])
 loc.int = as.integer(curc[,3])
 humanSNPlocs[[i]] = rbind(rsid=rsid.int, loc=loc.int)
# cat(i)
 }
}
@
 

Now get offsets for computing the chromosome-wide location values.
<<doco2,eval=FALSE>>=
require(org.Hs.eg.db)
chrl = org.Hs.egCHRLENGTHS
offs = c(0, cumsum(as.double(chrl[1:22])))

@
<<junk, eval=FALSE, echo=FALSE>>=
#setClass("snpLocs", representation(locEnv="environment",
#  offsets="numeric", organism="character", versions="character"))
#
#setMethod("show", "snpLocs", function(object) {
# cat("snpLocs instance, organism ", object@organism, "\n")
# cat("based on:\n")
# print(object@versions)
#})
@

Now we create the environment-based container instance:
<<docont,eval=FALSE>>=
el = new.env()
getv = function(x) installed.packages()[x, "Version"]
for (i in names(humanSNPlocs))
  assign(i, humanSNPlocs[[i]], el)
hsSnpLocs = new("snpLocs", locEnv=el, offsets=offs,
 organism="Hs", versions=c(
   org.Hs.eg.db=getv("org.Hs.eg.db"),
   SNPlocs.Hsapiens.dbSNP.20071016 = getv("SNPlocs.Hsapiens.dbSNP.20071016")))
@

This object will be saved in GGBase. 


\end{document}