Group features by complete-linkage similarity threshold

Reimplementation of MsFeatures::groupSimilarityMatrix with a fixed group-ID lookup when joining an existing group (named keys instead of integer positional indexing). Join rule is complete-linkage: a feature may join a group only if similarity to all current members is finite and >= threshold.

Usage

groupSimilarityMatrix_completeLinkage(x, threshold = 0.9, full = TRUE, ...)

Arguments

x

numeric square similarity matrix (symmetric when full = TRUE).

threshold

numeric(1). Minimum similarity to join / stay linked. Default 0.9.

full

logical(1). If FALSE, only the upper triangle is used.

...

Ignored; kept for call compatibility with MsFeatures.

Value

Integer vector of group IDs, length nrow(x).

Details

Available arguments: x, threshold, full, ....

See also

groupSimilarityMatrix_hclustAverage, xcms_group_feature_EIC