cluster_em_cross_cor: Cluster Expression-methylation cross-correlation

In tanaylab/methylayer: Layered modeling of tumor methylation

Description

Cluster Expression-methylation cross-correlation

Usage

cluster_em_cross_cor(
  em_list,
  k_meth,
  k_expr = k_meth,
  hc_exp = NULL,
  normal_meth = NULL
)

Arguments

em_list	output of em_cross_cor
k_meth	number of methylation clusters
k_expr	number of expression clusters
hc_exp	hclust object with existing clustering of the matrix columns

Value

a list with:

• "em_cross"Matrix with expression-methylation correlation values. Rows are loci and columns are genes

• meth_matMatrix with methylation values (filtered)

• expr_matMatrix with expression values (filtered)

• hc_methhclust object with clustering of the loci

• hc_exphclust object with clustering of the genes

• meth_clusttibble with cluster number for each row

• expr_clusttibble with cluster number for each column

• expr_modsmatrix with mean expression in every cluster for each sample

• meth_modsmatrix with mean methylation in every cluster for each sample

• expr_mods_locusmatrix with mean expression in every cluster for each locus

• meth_mods_genematrix with mean methylation in every cluster for each gene

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