inst/oldRsrc/egtset.R

In GGtools: software and data for analyses in genetics of gene expression

#
#setClass("egtSet", representation(gtlist="list", snpNames="list"), contains="eSet",
# prototype=prototype(new("ExpressionSet"), gtlist=list()))
#
#convertSS = function(smlSet, ffstub="ffsnp_") {
# ss = smList(smlSet)
# sn = lapply(ss, colnames)
# cn = names(ss)
# fn = paste(ffstub, cn, ".ff", sep="")
# ss = lapply(ss, function(x) {dimnames(x) <- NULL; x})
# ffrefs = lapply(1:length(ss), function(i) ff(ss[[i]], dim=dim(ss[[i]]), vmode="raw",
#		overwrite=TRUE, filename=fn[i]))
# tmp = lapply(ffrefs, function(x) close.ff(x))
# names(ffrefs) = cn
# ee = as(smlSet, "ExpressionSet")
# new("egtSet", assayData=assayData(ee),
#	phenoData=phenoData(ee),
#	experimentData=experimentData(ee),
#	protocolData=protocolData(ee),
#	featureData=featureData(ee),
#	annotation=annotation(ee),
#	gtlist=ffrefs,
#	snpNames=sn)
#}
#
#setMethod("show", "egtSet", function(object) {
# callNextMethod()
# cat("Genotype information in a list of ff of length", length(object@gtlist), "\n")
# cat(" SNP data ncols:\n  ")
# cat(selectSome(sapply(object@gtlist, ncol)))
# cat("\n")
# cat(" SNP names for first element:\n  ")
# cat(selectSome(object@snpNames[[1]]))
# cat("\n")
#})
#
#setMethod("exprs", "egtSet", function(object) {
# assayData(object)$exprs
#})
#
#setMethod("smList", "egtSet", function(x) {
# x@gtlist
#})
#
#setGeneric("getSNP", function(egts, chrind, tok) standardGeneric("getSNP"))
#setMethod("getSNP", c("egtSet", "ANY", "ScalarCharacter"), function(egts, chrind, tok) {
# sind = match(tok, egts@snpNames[[chrind]])
# smList(egts)[[chrind]][,sind,drop=FALSE]
#})
#
#setMethod("[", "egtSet", function(x, i, j, ..., drop=FALSE) {
# if (is(i, "chrnum")) {
#   if (!(i %in% names(smList(x)))) stop("requested chrnum not among smList elements")
#   x@gtlist = x@gtlist[i]
#   x@snpNames = x@snpNames[i]
#   return(x)
# }
# callNextMethod()
#})
#