Description Usage Arguments Value
Identify nodes in a hierarchical tree which qualify as clones. Identify 'hard' clones first, then expand them to 'soft' clones. Expansion may result in clone mergers. Based on hierarchical clustering, identify the hard/soft clones.
1 2 | find_clones(hc, fdrthresh = -2, sharemin = 0.85, nshare = 3, bymax = T,
climbfromsize = 2, climbtoshare = 3)
|
hc |
An hclust object with additional items generated by |
fdrthresh |
maximal allowed value for log10(FDR) for any pair of leaves in a clone node. Default: -2. |
sharemin |
A feature is considered 'widely shared' if present in sharemin fraction of leaves in a node.Default: 0.90. |
nshare |
Minimal number of 'widely shared' features in a hard clone. Default: 3. |
bymax |
Logical. If TRUE (default), use maximal, and otherwise mean, FDR for the node as a criterion for a hard clone. |
climbfromsize |
An integer: minimal size of a hard clone allowed to be expanded |
climbtoshare |
An integer: expand the clone as long as the number of widely shared features is at least this value |
An hclust object, with hard/soft clones indicated
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