Get DMPs

get_DMPs returns a df with annotated statistics for each CpG

get_DMPs(path, patient_id, sample_id, df, prob = 0.99, n_cores)

Arguments

path

Complete path to the CAMDAC methylation output directory fir this sample

patient_id

Character string containting the patient number

sample_id

Character variable with the tumour sample_id

df

A data.table with pure, bulk and normal methylation info

prob

Numerical value representing the threshold for statistically significant DMP (default is p=0.99)

n_cores

Number of cores to do the statistical testing over

Value

A data.table object with all the CpG loci, their coverage, counts methylated and methylation rate