| bf8acd05 |
##How to make the initialization platform-specific?
|
| bc16b510 |
setMethod("initialize", "SnpSuperSet",
|
| bf8acd05 |
function(.Object,
|
| bc16b510 |
assayData,
|
| 96d10c6e |
call=new("matrix"),
callProbability=new("matrix"),
|
| bc16b510 |
alleleA=new("matrix"),
alleleB=new("matrix"),
featureData,
|
| bf8acd05 |
annotation,
|
| bc16b510 |
...){
if(!missing(assayData)){
.Object <- callNextMethod(.Object, assayData=assayData,...)
|
| bf8acd05 |
} else{
|
| bc16b510 |
ad <- assayDataNew("lockedEnvironment",
call=call,
callProbability=callProbability,
alleleA=alleleA,
alleleB=alleleB)
.Object <- callNextMethod(.Object,
assayData=ad, ...)
}
if(missing(annotation)){
stop("must specify annotation")
} else{
stopifnot(isValidCdfName(annotation))
.Object@annotation <- annotation
}
|
| bf8acd05 |
if (missing(featureData)){
|
| bc16b510 |
featureData(.Object) <- annotatedDataFrameFrom(call, byrow=TRUE)
|
| bf8acd05 |
} else{
featureData(.Object) <- featureData
}
|
| 96d10c6e |
## Do after annotation has been assigned
if(!(all(c("chromosome", "position", "isSnp") %in% colnames(.Object@featureData)))){
##update the featureData
|
| bc16b510 |
.Object@featureData <- addFeatureAnnotation.SnpSuperSet(.Object)
|
| 96d10c6e |
}
|
| bf8acd05 |
.Object
})
|
| 96d10c6e |
|
| bc16b510 |
setMethod("addFeatureAnnotation", "SnpSuperSet", function(object, ...){
addFeatureAnnotation.SnpSuperSet(object, ...)
|
| 96d10c6e |
})
|
| bc16b510 |
getParam.SnpSuperSet <- function(object, name, batch){
|
| bf8acd05 |
label <- paste(name, batch, sep="_")
colindex <- grep(label, fvarLabels(object))
if(length(colindex) == 1){
param <- fData(object)[, colindex]
}
if(length(colindex) < 1){
param <- NULL
}
if(is.na(colindex)){
stop(paste(label, " not found in object"))
}
if(length(colindex) > 1){
stop(paste(label, " not unique"))
}
return(param)
}
|
| 96d10c6e |
|
| bf8acd05 |
|
| bc16b510 |
setMethod("splitByChromosome", "SnpSuperSet", function(object, cnOptions){
|
| bf8acd05 |
tmpdir <- cnOptions[["tmpdir"]]
outdir <- cnOptions[["outdir"]]
save.it <- cnOptions[["save.it"]]
path <- system.file("extdata", package=paste(annotation(object), "Crlmm", sep=""))
load(file.path(path, "snpProbes.rda"))
snpProbes <- get("snpProbes")
load(file.path(path, "cnProbes.rda"))
cnProbes <- get("cnProbes")
k <- grep("chr", colnames(snpProbes))
if(length(k) < 1) stop("chr or chromosome not in colnames(snpProbes)")
for(CHR in 1:24){
cat("Chromosome ", CHR, "\n")
snps <- rownames(snpProbes)[snpProbes[, k] == CHR]
cnps <- rownames(cnProbes)[cnProbes[, k] == CHR]
index <- c(match(snps, featureNames(object)),
match(cnps, featureNames(object)))
index <- index[!is.na(index)]
callSetPlus <- object[index, ]
if(CHR != 24){
|
| 96d10c6e |
cnSet <- computeCopynumber(callSetPlus, cnOptions)
|
| bf8acd05 |
} else{
message("Copy number estimates not available for chromosome Y. Saving only the 'callSetPlus' object for this chromosome")
save(callSetPlus, file=file.path(outdir, paste("callSetPlus_", CHR, ".rda", sep="")))
}
if(cnOptions[["hiddenMarkovModel"]] & CHR != 24){
|
| 96d10c6e |
cnSet <- computeHmm(cnSet, cnOptions)
}
save(cnSet, file=file.path(outdir, paste("cnSet_", CHR, ".rda", sep="")))
saved.objects <- list.files(outdir, pattern="cnSet", full.names=TRUE)
## } else{ ## save crlmmSet to outdir
## save(cnSet, file=file.path(outdir, paste("cnSet_", CHR, ".rda", sep="")))
## saved.objects <- list.files(outdir, pattern="cnSet", full.names=TRUE)
## }
|
| bf8acd05 |
}
saved.objects
})
|
| 96d10c6e |
|
| bc16b510 |
setMethod("computeCopynumber", "SnpSuperSet",
|
| bf8acd05 |
function(object, cnOptions){
|
| bc16b510 |
computeCopynumber.SnpSuperSet(object, cnOptions)
|
| bf8acd05 |
})
|
| 96d10c6e |
|
| bc16b510 |
##gtConfidence <- function(object) 1-exp(-confs(object)/1000)
|
| bf8acd05 |
|
