Assign bins

annotate_DMRs returns the df with the annotation for each CpG

get_DMRs(
  path,
  patient_id,
  sample_id,
  dt,
  anno_list,
  min_DMP_counts,
  min_consec_DMP,
  n_cores,
  bulk = FALSE
)

Arguments

path

Character string of the output directory

patient_id

Character string containting the patient_id ID

sample_id

Character string containting the sample ID.

dt

dataframe where each CG is a row with DMP info.

anno_list

A data.table object containing annotated genomic bins including genes, exons, introns, UTRs, CGI, CGI shores, CGI shelves, promoters or enhancers

min_DMP_counts

Numerical - number of DMPs required in a DMR

min_consec_DMP

Numerical - number of consecutive DMPs required in a DMR

n_cores

number of cores for parallel processing

Value

A dataframe for each sample_id with the copy number calls added