deconv_TME: Deconvolute TME (tumor microenvironment) effects from...
In tanaylab/methylayer: Layered modeling of tumor methylation

Deconvolute TME (tumor microenvironment) effects from methylation data

deconv_TME(
  meth_mat,
  expr_mat,
  raw_meth_mat,
  min_meth = 0.1,
  max_meth = 0.9,
  min_expr = NULL,
  meth_cor_thresh = 0.25,
  expr_cor_thresh = 0.25,
  min_sd = NULL,
  k = NULL,
  k_meth = 30,
  k_expr = k_meth,
  caf_gene = "CAV1",
  immune_gene = "CD3D",
  scores_cor_thresh = 0.3,
  ...
)

`meth_mat`	Matrix with methylation values to use for TME inference (usually - promoter methylation). Each row is a locus and each column is a sample. This can be a different matrix than `raw_meth_mat`.
`expr_mat`	Matrix with expression values. Each row is a gene and each column is a sample.
`raw_meth_mat`	Matrix with methylation values to deconvolute. Each row is a locus and each column is a sample. This can be a different matrix than `meth_mat`.
`min_meth`	minimal locus average methylation
`max_meth`	maximal locus average methylation
`min_expr`	minimal expression level. Only genes with at least one sample with expression above min_expr would be included.
`meth_cor_thresh`	minimal correlation level of a locus. Only loci with at least one correlation above the threshold will be included.
`expr_cor_thresh`	minimal correlation level of a gene. Only genes with at least one correlation above the threshold will be included.
`min_sd`	minimal standard deviation per locus.
`k`	k parameter for knn
`k_meth`	number of methylation clusters when clustering expression-methylation data
`k_expr`	number of expression clusters when clustering expression-methylation data
`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")
`scores_cor_thresh`	minimal (anti) correlation of loci methylation to TME expression scores in order to create TME methylatoon scores
`...`	additional parameters to `em_cross_cor`

a list with:

norm_methMatrix with normalized methylation values of raw_meth_mat
tme_featuresData frame with Immune and CAF expression and methylation signatures per sample
(tme_loci)list with intervals set of loci that were included in the immune and CAF methylation scores
em_crossList as returned from em_cross_cor. Mainly includes a matrix with expression-methylation correlation values that were used for the deconvolution algorithm, where rows are loci and columns are genes
em_cross_clustClustering of expression-methylation correlation data, as returned from cluster_em_cross_cor