Get candidates for promoters that are regulated by methylation in cis

Get candidates for promoters that are regulated by methylation in cis

cis_em_promoters(
  meth_mat,
  expr_mat,
  promoter_intervs,
  k_locus_rank = 2,
  min_samples = 100,
  spearman = FALSE
)

Arguments

meth_mat	Matrix with methylation values. Each row is a promoter 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.
promoter_intervs	intervals set with additional "name" column. In case of duplicate names or coordinates the first one in the matrix will be used. Only intervals that are within promoter_intervs would be used.
k_locus_rank	rank of the correlation to extract for each promoter. For example, if k_locus_rank = 2 the second best correlation would be extracted for every promoter in the field kth
min_samples	minimal number of samples per gene (both expression and methylation). Default is 100.
spearman	use spearman correlation (if FALSE - use pearson)

Value

dataframe with the following columns:

• namename of the gene

• (chrom,start,end)coordinates of the gene promoter

• rankrank of the correlation of the gene with it's promoter

• corcorrelation of the gene with it's promoter

• kthk_locus_rankth best correlation of the gene with a promoter

• fdrfalse discovery rate for detecting the cis-raget with rank value <= rank. Assuming independence between expression and methylation, the false discovery rate (FDR) for detecting the cis-target (diagonal value) with rank value <= k was defined as k / m, where m is the number of observed genes having cis-target (diagonal value) with rank value <= k.