Compute the tumour methylation rate

compute_tumour_methylome returns the data.table dt annotated with CAMDAC pure tumour methylation rates

compute_tumour_methylome(dt, p, min_cov_t = 3, sex, build)

Arguments

dt

data.table object with each CpG and their coverage, counts methylated, methylation rate and copy number and matched normal methylation info

p

Numerical - Sample purity estimates

min_cov_t

Numerical - Minimum tumour coverage

sex

Character variable with the patient expressed as "XX" for female or "XY" for male.

build

Character variable corresponding to the reference genome used for alignment.

Value

A dataframe for each sample_id with the tumour methylome added