getMotifClustering

Retrieve motif clustering of TF motifs

getMotifClustering(
  k = 0,
  distM = NULL,
  assembly = "hg38",
  motifs = "jaspar",
  clusterMethod = "pam"
)

Arguments

k

number of clusters. k<1 will result in an automatically selected clustering which is precomputed and stored in ChrAccR. For distMethod=="jaspar" and clusterMethod=="pam" this corresponds to the k corresponding to the best silhouette value before a drop (in the silhouette elbow-curve) occurs

distM

distance matrix (dist object) containing motif dissimilarities/distances. Only required if k>0.

assembly

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. k<1).

motifs

a character string specifying the motif set (currently only "jaspar" is supported)

clusterMethod

method to be used for motif clustering (currently only 'pam' (PAM - partitioning around medoids) is supported)

Value

a list structure containing the clustering result

Author

Fabian Mueller