get_purity: Calculate purity or tumor content samples
In romagnolid/PAMES: Purity Assessment from clonal MEthylation Sites

get_purity

R Documentation

Calculate purity or tumor content samples

Description

Estimate the proportion of cancer cells in the admixture of cells forming the tumor microenvironment or the fraction of ctDNA in cfDNA samples.

Usage

get_purity(tumor_table, info_sites)

Arguments

`tumor_table`	A matrix of beta-values
`info_sites`	A data.frame reporting a set of informative sites generated by `find_informative_sites` or `find_informative_regions`.

Value

A data.frame with purity scores.

Examples

purity <- get_purity(tumor_toy_data,
 info_sites=data.frame(Probe=c("CpG_00001","CpG_00010","CpG_00020",
     "CpG_00015","CpG_00030","CpG_00045"), Site_type=rep(c("hyper","hypo"), each=3)))

romagnolid/PAMES documentation built on Dec. 7, 2022, 10:37 a.m.