clusterSignalMatrices: clusterSignalMatrices: clusters the regions of a (set of)...

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

clusterSignalMatrices: clusters the regions of a (set of) signal matrices.

Description

clusterSignalMatrices: clusters the regions of a (set of) signal matrices.

Usage

clusterSignalMatrices(
  ml,
  k,
  scaleRows = FALSE,
  scaleCols = FALSE,
  use = c("enrich", "full", "max", "center"),
  by = rep(1L, length(ml)),
  assay = 1L,
  trim = c(0.05, 0.95),
  nstart = 3,
  ...
)

Arguments

ml	A named list of signal matrices or an EnrichmentSE object as produced by signal2Matrix
k	The number of clusters to generate
scaleRows	Logical; whether to scale rows for clustering
scaleCols	Logical; whether to scale columns (i.e. signals/samples)
use	What values to use for clustering. By default, uses enriched_score. Other options are 'full' (uses the full signal for clustering), 'max' (uses the maximum value in the region), or 'center' (use the value at the center of the region).
by	Optional factor/character/integer vector of the same length as 'ml'. When scaling rows, this can be used to indicate which rows should be scaled together.
assay	Assay to use (ignored unless 'ml' is an ESE object)
trim	Values to trim (applied individually for each signal matrix)
nstart	Number of starts for k-means clustering
...	Passed to 'kmeans'

Value

If 'k' is of length 1, a vector of cluster labels, corresponding to the rows of 'ml'. If 'length(k)>1', a list of two data.frames containing: 1) the cluster labels at the different resolutions, and 2) the variance explained by clusters at each resolution.

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.