Estimates the cancer cell fraction (CCF) based on minor and major allele copy numbers, tumor purity, and observed minor-allele frequency (MAF).
Usage
CcfLOH(minor, major, rho, MAF)
Arguments
- minor
Numeric. Minor allele copy number.
- major
Numeric. Major allele copy number.
- rho
Numeric. Tumor purity (fraction between 0 and 1).
- MAF
Numeric. Observed B-allele frequency.
Value
Numeric. The estimated cancer cell fraction (CCF), with Inf replaced by 1, -Inf and NA replaced by 0.
Details
The expected MAF is calculated as MAF_ex = minor / (minor + major).
The formula for CCF is:
ccf = (MAF - 0.5) / ((MAF_ex - 0.5) * rho)
If CCF is Inf, returns 1; if -Inf or NA, returns 0.
Examples
CcfLOH(minor = 1, major = 2, rho = 0.7, MAF = 0.6)
#> [1] -0.8571429
