normalize_immune_cafs_meth: Normalize methylation matrix for immune and CAF signatures

In tanaylab/methylayer: Layered modeling of tumor methylation

Description

Normalize methylation matrix for immune and CAF signatures

Usage

normalize_immune_cafs_meth(
  em_clust,
  k,
  meth_mat = em_clust$meth_mat,
  scale_feats = TRUE,
  caf_gene = "CAV1",
  immune_gene = "CD3D"
)

Arguments

em_clust	output of cluster_em_cross_cor
k	k parameter for knn
scale_feats	scale features (recommended)
caf_gene	name of gene that is inside the CAF cluster (default: "CAV1")
immune_gene	name of gene that is inside the immune cluster (default: "CD3D")

Value

normalized methylation matrix

tanaylab/methylayer documentation built on Dec. 23, 2021, 7:45 a.m.