get_similarity_rank_matrix

Given a lower triangular similarity matrix, construct a distance matrix where the rows are the ranks of the column cases with respect to similarity to the row case. If relative similarity is of interest, this rank-transformation may reduce bias in favour of high similarity scores in downstream analysis.

Calculate similarity between ontological terms and sets of ontological terms based on term information content and assess statistical significance of similarity in the context of a collection of terms sets - Greene et al. 2017 <doi:10.1093/bioinformatics/btw763>.

Daniel Greene

ontologySimilarity

Calculating Ontological Similarities

get_similarity_rank_matrix function

<dl><dt>similarity_matrix</dt>
<dd>Lower triangular numeric matrix of similarities, where the rownames and colnames are identical to the case IDs.</dd>
<dt>symmetric</dt>
<dd>Logical value determining whether to `symmetrify' resultant matrix by averaging rank similarity of A -&gt; B and B -&gt; A.</dd></dl>

Arguments

Get matrix of similarity rank from similarity matrix — get_similarity_rank_matrix

<dl>

<dt>similarity_matrix</dt>
<dd>Lower triangular numeric matrix of similarities, where the rownames and colnames are identical to the case IDs.</dd>


<dt>symmetric</dt>
<dd>Logical value determining whether to `symmetrify' resultant matrix by averaging rank similarity of A -&gt; B and B -&gt; A.</dd>

</dl>

get_similarity_rank_matrix: Get matrix of similarity rank from similarity matrix

Description

Usage

Value

Arguments