Nothing
format.smpl.name <- function(name, break.every = 20, break.char = "<br/>") {
gsub(sprintf("(.{%s})", break.every), paste0("\\1", break.char), name)
}
dataType$set("public", "rawAdp",
NA,
overwrite = TRUE)
dataType$set("public", "PreprocessAdp",
function(smooth, smooth.method, normqPCR.method) {
if (!is.environment(self$rawAdp)) {
self$rawAdp <- private$.adp$copy()
}
private$.adp$fpoints$fluor <-
CPP(self$rawAdp$fpoints$cyc,
self$rawAdp$fpoints$fluor,
smoother = smooth,
method = smooth.method,
method.norm = normqPCR.method)[[1]]
},
overwrite = TRUE)
dataType$set("public", "UndoPreprocessAdp",
function() {
if (!is.environment(self$rawAdp)) {
self$rawAdp <- private$.adp$copy()
} else {
private$.adp$fpoints$fluor <-
self$rawAdp$fpoints$fluor
}
NULL
},
overwrite = TRUE)
dataType$set("public", "CalcCq",
#calculate Ct
function(cq.method, th.level, auto.th) {
fdt <- self$adp$fpoints
switch(cq.method,
none = {
cq <- self$cq
quantFluor <- self$quantFluor
},
th = {
th <- th.cyc(fdt$cyc, fdt$fluor, r = th.level,
auto = auto.th)
cq <- th[1, 1]
quantFluor <- th[1, 2]
if (is.na(cq)) {
cq <- NULL
quantFluor <- NULL
}},
sdm = {
res <- diffQ2(data.frame(fdt$cyc, fdt$fluor), inder = TRUE, warn = FALSE)
cq <- res$xTm1.2.D2[1]
cyc.before.i <- tail(which(fdt$cyc < res$xTm1.2.D2[1]), 1)
if (cyc.before.i == length(fdt$cyc)) {
quantFluor <- fdt$fluor[cyc.before.i]
} else {
delta <- (res$xTm1.2.D2[1] - fdt$cyc[cyc.before.i]) /
(fdt$cyc[cyc.before.i + 1] - fdt$cyc[cyc.before.i])
quantFluor <- (fdt$fluor[cyc.before.i + 1] - fdt$fluor[cyc.before.i]) *
delta + fdt$fluor[cyc.before.i]
}
})
self$cq <- cq
self$quantFluor <- quantFluor
},
overwrite = TRUE)
dataType$set("public",
"DetectHook",
function(hookDetectionMethod, sample, position) {
hookRes <-
if (hookDetectionMethod == "hookreg" || hookDetectionMethod == "both") {
as.logical(hookreg(x = self$adp$fpoints[["cyc"]],
y = self$adp$fpoints[["fluor"]])[["hook"]])
} else {
FALSE
}
hookNLRes <-
if (hookDetectionMethod == "hookregNL" || hookDetectionMethod == "both") {
as.logical(hookregNL(x = self$adp$fpoints[["cyc"]],
y = self$adp$fpoints[["fluor"]])[["hook"]])
} else {
FALSE
}
if (hookRes && hookNLRes) {
sample$annotation <-
c(sample$annotation,
annotationType$new(sprintf("%s_hookDetectionMethod",position),
"both"))
} else {
if (hookRes) {
sample$annotation <-
c(sample$annotation,
annotationType$new(sprintf("%s_hookDetectionMethod",position),
"hookreg"))
}
if (hookNLRes) {
sample$annotation <-
c(sample$annotation,
annotationType$new(sprintf("%s_hookDetectionMethod",position),
"hookregNL"))
}
}
if (hookRes || hookNLRes) {
sample$annotation <-
c(sample$annotation,
annotationType$new(sprintf("%s_hook", position),
"TRUE"))
} else {
sample$annotation <-
c(sample$annotation,
annotationType$new(sprintf("%s_hookDetectionMethod",position),
"hookDetectionMethod"))
sample$annotation <-
c(sample$annotation,
annotationType$new(sprintf("%s_hook", position),
"FALSE"))
}
""
},
overwrite = TRUE)
dataType$set("public", "rawMdp",
NA,
overwrite = TRUE)
dataType$set("public", "PreprocessMdp",
function(bgadj, bg, minmax, df.fact) {
if (!is.environment(self$rawMdp)) {
self$rawMdp <- private$.mdp$copy()
}
private$.mdp$fpoints$fluor <-
mcaSmoother(self$rawMdp$fpoints$tmp,
self$rawMdp$fpoints$fluor,
bgadj = bgadj,
bg = bg,
minmax = minmax,
df.fact = df.fact)[, 2]
},
overwrite = TRUE)
dataType$set("public", "UndoPreprocessMdp",
function() {
if (!is.environment(self$rawMdp)) {
self$rawMdp <- private$.mdp$copy()
} else {
private$.mdp$fpoints$fluor <-
self$rawMdp$fpoints$fluor
}
NULL
},
overwrite = TRUE)
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