Retrieve motif clustering of TF motifs
getMotifClustering( k = 0, distM = NULL, assembly = "hg38", motifs = "jaspar", clusterMethod = "pam" )
number of clusters.
k<1 will result in an automatically selected clustering which is precomputed and stored in
clusterMethod=="pam" this corresponds to the k corresponding to the best silhouette value before a drop (in the silhouette elbow-curve) occurs
distance matrix (
dist object) containing motif dissimilarities/distances. Only required if
genome assembly for which the motifs dissimilarity should be retrieved. Only the species information
of the assembly is really relevant. Can be
"vert" for all vertebrate motifs. Only required if for automatic mode (i.e.
a character string specifying the motif set (currently only "jaspar" is supported)
method to be used for motif clustering (currently only
'pam' (PAM - partitioning around medoids) is supported)
a list structure containing the clustering result