Nothing
## .isMSImageObject
#' @importFrom methods is
.isMSImageObject <- function(x) {
return(is(object = x, class2 = "ms.image"))
}
## .isMSIDatasetObject
#' @importFrom methods is
.isMSIDatasetObject <- function(x) {
return(is(object = x, class2 = "msi.dataset"))
}
## .isBinary
.isBinary <- function(x) {
.stopIfNotValidMSImage(x)
if (all(unique(c(x@values)) %in% c(0, 1))) {
return(TRUE)
} else {
return(FALSE)
}
}
## .isPeakFilter
.isPeakFilter <- function(x) {
if (is.null(attr(x, "peak.filter"))) {
return(FALSE)
}
if (!attr(x, "peak.filter")) {
return(FALSE)
}
return(TRUE)
}
## .stopIfNotValidMSImage
.stopIfNotValidMSImage <- function(x) {
if (!.isMSImageObject(x)) {
stop("Not a SPUTNIK::ms.image object.")
}
return(invisible(NULL))
}
## .stopIfNotValidMSIDataset
.stopIfNotValidMSIDataset <- function(x) {
if (!.isMSIDatasetObject(x)) {
stop("Not a SPUTNIK::msi.dataset object.")
}
return(invisible(NULL))
}
## .stopIfNotValidPeakFilter
.stopIfNotValidPeakFilter <- function(x) {
if (!.isPeakFilter(x)) {
stop("Not a valid peak.filter result.")
}
return(invisible(NULL))
}
## .stopIfNotValidGlobalMethod
.stopIfNotValidGlobalMethod <- function(x) {
accept.values <- c("pearson", "spearman", "ssim", "nmi")
if (!any(x %in% accept.values)) {
stop(
"Accepted method values are: ",
paste0(accept.values, collapse = ", "), "."
)
}
return(invisible(NULL))
}
## Validity function for m/z vector
.checkValidMZ <- function(mz) {
if (!is.numeric(mz)) {
cat("M/Z must be numeric\n")
return(FALSE)
}
if (length(mz) != length(unique(mz))) {
cat("M/Z contains duplicated values.\n")
return(FALSE)
}
if (any(diff(mz) <= 0)) {
cat("M/Z values must be sorted.\n")
return(FALSE)
}
return(TRUE)
}
## Validity function for intensity matrix
.checkValidIntensityMatrix <- function(intensityMatrix, showWarnings = FALSE) {
if (!is.matrix(intensityMatrix) || !is.numeric(intensityMatrix)) {
cat("Intensity matrix must be a numeric matrix.\n")
return(FALSE)
}
if (length(dim(intensityMatrix)) != 2) {
cat("Intensity matrix must be 2-dimensional.\n")
return(FALSE)
}
if (any(!is.finite(intensityMatrix))) {
cat("Intensity matrix must contain finite values.\n")
return(FALSE)
}
if (any(intensityMatrix < 0)) {
if (showWarnings) {
cat("WARNING: Intensity matrix contains negative values.\n")
}
}
if (any(intensityMatrix == 0)) {
if (showWarnings) {
cat("WARNING: Zeros present in the intensity matrix. A positive offset
may be necessary for normalization or variance stabilizing transformation.\n")
}
}
return(TRUE)
}
## Validity function for image shape
.checkValidImageShape <- function(x) {
if (!is.finite(x)) {
cat("Shape must be finite.\n")
return(FALSE)
}
if (!is.numeric(x) || length(x) != 1) {
cat("Shape must be a numeric value.\n")
return(FALSE)
}
if (x <= 0) {
cat("Shape must be a positive number.\n")
return(FALSE)
}
return(TRUE)
}
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