Get candidates non-promoter cis regulation

cis_em_genomic(
  meth_mat,
  expr_mat,
  gene_tss,
  min_samples = 100,
  max_k = 50,
  max_dist = 500000,
  min_dist = 200,
  spearman = FALSE,
  parallel = FALSE
)

Arguments

meth_mat	Matrix with methylation values. Each row is a locus and each column is a sample. Rownames should contain "chrom", "start" and "end" separated by "_"
expr_mat	Matrix with expression values. Each row is a gene and each column is a sample.
gene_tss	intervals set with additional "name" column with transcription start site (TSS) for each gene. Used for allocating a genomic coordinate for each gene. In case of duplicate names or coordinates the first one in the matrix will be used.
min_samples	minimal number of samples per gene (both expression and methylation). Default is 100.
max_k	maximal number of genes to report per locus. Default is 50. Note that for efficiency (memory and computation) it is best to keep this number small.
max_dist	maximal distance from TSS to consider "cis" (used for FDR computations)
min_dist	minimal distance from TSS (in order to exclude promoter regulation). Used for FDR computation.
spearman	use spearman correlation (if FALSE - use pearson)
parallel	use mclapply for computation of ranks. Note that for large matrices forking might fail due to lack of memory and therefore parallel should be set to FALSE.