plotLMC.reference: plotLMC.reference

In lutsik/MeDeCom: Decomposition of heterogeneous methylomes

plotLMC.reference

Description

This routine uses a reference methylome, together with an annotation, and calls plotLMCs for the matching postions

Usage

plotLMC.reference(
  medecom.set,
  ref.meth,
  ann.md,
  cg_subset = medecom.set@parameters$cg_subsets[1],
  K = medecom.set@parameters$Ks[1],
  lambda = medecom.set@parameters$lambdas[1],
  ann.ref = NULL,
  type = "dendrogram",
  chrom.col = "Chromosome",
  start.col = "Start",
  end.col = "End",
  ct.color.column = "cell_type"
)

Arguments

medecom.set	An object of type MeDeComSet
ref.meth	Reference methylome in the form of a matrix of a RnBSet
ann.md	Genomic annotation for the CpG sites present in medecom.set
cg_subset	The cg_subset of interest
K	K value
lambda	lambda value
ann.ref	Genomic annotation for the CpG sites in the referenc methylome. Can be omitted, if ref.meth is an RnBSet object
type	Plot type, see plotLMCs
chrom.col	The chromosome column name in ann.md and ann.ref
start.col	The start column name in ann.md and ann.ref
end.col	The end column name in ann.md and ann.ref
ct.color.column	A column name in the phenotypic information of ref.meth to be shown in the clustering

Author(s)

Michael Scherer

lutsik/MeDeCom documentation built on July 15, 2024, 4:51 a.m.