getMotifClustering: getMotifClustering

In demuellae/ChrAccR: Analyzing chromatin accessibility data in R

Description

Retrieve motif clustering of TF motifs

Usage

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	either a character string (currently only "jaspar" is supported) or an object containing PWMs that can be used by motifmatchr::matchMotifs (PWMatrixList object)
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(s)

Fabian Mueller

demuellae/ChrAccR documentation built on Jan. 20, 2020, 3:03 a.m.