Calculate Expression-methylation cross-correlation

Calculate Expression-methylation cross-correlation

em_cross_cor(
  meth_mat,
  expr_mat,
  min_meth = NULL,
  max_meth = NULL,
  min_expr = NULL,
  min_sd = NULL,
  samples = NULL,
  max_na = NULL,
  meth_cor_thresh = NULL,
  expr_cor_thresh = NULL
)

Arguments

meth_mat

Matrix with methylation values. Each row is a locus and each column is a sample.
expr_mat

Matrix with expression values. Each row is a gene and each column is a sample.
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.
min_sd

minimal standard deviation per locus.
samples

names of samples to include. If NULL - all samples that have both expression and methylation data would be included.
max_na

maximal number of NAs allowed per locus.
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.

Value

a list with:

  • em_crossMatrix with expression-methylation correlation values. Rows are loci and columns are genes

  • meth_matMatrix with methylation values (filtered)

  • expr_matMatrix with expression values (filtered)

Examples


if (FALSE) {
 init_tcga_brca_example()
 em_list <- get_em_cross(brca_meth_mat, brca_expr_mat, min_meth = 0.1, max_meth = 0.9, meth_cor_thresh = 0.25, expr_cor_thresh = 0.25, min_expr = 2, min_sd = 0.05, max_na = 0)
  

}