Make CAMDAC methylation panel from a matrix of beta values

Make CAMDAC methylation panel from a matrix of beta values

panel_meth_from_beta(
  mat,
  chrom,
  start,
  end,
  cov,
  props,
  cores,
  min_samples = 1,
  max_sd = 1
)

Arguments

mat

Matrix of beta values. Rows are CpGs, columns are samples

chrom

Vector of chromosome names

start

Vector of CpG start positions

end

Vector of CpG end positions

cov

Vector of coverage values to give each CpG site. If a matrix is provided, coverage is calculated as the sum of reads for each site.

cores

Number of cores to use for calculating HDI

min_samples

Minimum number of samples that must have a non-NA value for a CpG site to be included in panel

max_sd

Maximum standard deviation of methylation for a site to be included in panel.