Nothing
#' Check validity of parameters to the `MSstatsImport` function.
#' @inheritParams MSstatsImport
#' @return none, throws an error if any of the assertions fail
#' @keywords internal
.checkMSstatsParams = function(input, annotation,
feature_columns,
remove_shared_peptides,
remove_single_feature_proteins,
feature_cleaning) {
checkmate::assertDataTable(input)
checkmate::assertTRUE(is.character(annotation) |
inherits(annotation, "data.frame") |
is.null(annotation))
checkmate::assertCharacter(feature_columns, min.len = 1)
checkmate::assertLogical(remove_shared_peptides)
checkmate::assertLogical(
feature_cleaning[["remove_features_with_few_measurements"]],
)
checkmate::assertLogical(remove_single_feature_proteins)
checkmate::assertLogical(feature_cleaning[["remove_psms_with_all_missing"]],
null.ok = TRUE)
checkmate::assertFunction(feature_cleaning[["summarize_multiple_psms"]])
}
#' Select an available options from a set of possibilities
#' @param possibilities possible legal values of a variable
#' @param option_set set of values that includes one of the `possibilities`
#' @param fall_back if there is none of the `possibilities` in `option_set`,
#' or there are multiple hits, default to `fall_back`
#' @return same as option_set, usually character
#' @keywords internal
.findAvailable = function(possibilities, option_set, fall_back = NULL) {
chosen = option_set[option_set %in% possibilities]
if (length(chosen) != 1L) {
if (is.null(fall_back)) {
NULL
} else {
if (fall_back %in% possibilities) {
fall_back
} else {
NULL
}
}
} else {
chosen
}
}
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