Nothing
## AbstractMassObject
setMethod(f="transformIntensity",
signature=signature(object="AbstractMassObject"),
definition=function(object,
method=c("sqrt", "log", "log2", "log10")) {
## empty spectrum?
if (.isEmptyWarning(object)) {
return(object)
}
method <- match.arg(method)
fun <- switch(method,
"sqrt" = {
sqrt
},
"log" = {
log
},
"log2" = {
log2
},
"log10" = {
log10
}
)
.transformIntensity(object, fun=fun)
})
## AbstractMassObject
setMethod(f=".transformIntensity",
signature=signature(object="AbstractMassObject"),
definition=function(object, fun, na.rm=TRUE, ...) {
if (!isEmpty(object)) {
fun <- match.fun(fun)
object@intensity <- fun(object@intensity, ...)
if (na.rm) {
naIdx <- which(!is.na(object@intensity))
object@intensity <- object@intensity[naIdx]
object@mass <- object@mass[naIdx]
}
object <- .replaceNegativeIntensityValues(object)
}
object
})
## list
setMethod(f="transformIntensity",
signature=signature(object="list"),
definition=function(object, ...) {
## test arguments
.stopIfNotIsMassObjectList(object)
.lapply(object, transformIntensity, ...)
})
## list
setMethod(f=".transformIntensity",
signature=signature(object="list"),
definition=function(object, ...) {
## test arguments
.stopIfNotIsMassObjectList(object)
.lapply(object, .transformIntensity, ...)
})
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