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Add Manual featurefilt mode to processing() and feature_filtering(). #125

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Add Manual featurefilt mode to processing() and feature_filtering(). #125

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7 changes: 6 additions & 1 deletion R/HelperChecks.R
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Original file line number Diff line number Diff line change
Expand Up @@ -563,7 +563,7 @@ check_param_feature_filtering <- function(
featurefilt = "Modified",
cutoff_featurefilt = 0.8
) {
Feature_Filtering_options <- c("Standard", "Modified")
Feature_Filtering_options <- c("Standard", "Modified", "Manual")

if (!(is.null(featurefilt) || featurefilt %in% Feature_Filtering_options)) {
message <-
Expand All @@ -576,6 +576,11 @@ check_param_feature_filtering <- function(
stop(message)
}

# Note: whether metadata_feature is usable for featurefilt = "Manual" is
# not validated here, since an unusable metadata_feature is not an error
# — feature_filtering() falls back to "Modified"/"Standard" with a
# warning instead. cutoff_featurefilt is still validated unconditionally,
# since it may end up being used after such a fallback.
if (
!is.numeric(cutoff_featurefilt) |
length(cutoff_featurefilt) != 1 |
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