Format methylation rates format_methylation_df

Format methylation rates format_methylation_df

format_methylation_df(
  dt,
  sample_id,
  normal_ids,
  path_output,
  n_cores,
  suffix,
  trim = FALSE
)

Arguments

dt

data.table containing the methylation information for each CpG

sample_id

sample ID

normal_ids

sample ID of normal sample(s)

path_output

output directory

n_cores

number of threads for HDI calculation

suffix

string containing the column names suffix for normal samples This is to distinguish between the proxy supplied for the normal infiltrates for use in deconvolution and the normal cell of origin for use in DMP/DMR calling

trim

Logical value establishing whether regions with extremely high coverage be trimmed or not

Value

A GRanges object with all the CpG loci, their coverage, counts methylated and methylation rate