plotLMC.reference | R Documentation |
This routine uses a reference methylome, together with an annotation, and calls plotLMCs for the matching postions
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")
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 |
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 |
Michael Scherer
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