Cluster CpGs into annotated bins

bin_CpGs returns the df with the annotation for each CpG

bin_CpGs(path, patient_id, sample_id, dt, anno_list, n_cores)

Arguments

path

Character string of the output directory

patient_id

Character string containting the patient ID

sample_id

Character string containting the sample ID.

dt

data.table 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

n_cores

number of cores for parallel processing

Value

A dataframe for each sample_id with the copy number calls added