Calculate Cancer Cell Fraction (CCF)

Computes the cancer cell fraction (CCF) based on total copy number, mutation multiplicity, tumor purity, and integer copy number.

Usage

Calccf(CN, mu, rho, C_i)

Arguments

CN

Numeric. The total copy number in the segment.

mu

Numeric. Diploid coverage scale factor (e.g. A value of 1 indicates that the segment mean from GATK does not require adjustment. Additionally, the pseudo-diploid coverage is set to 100.).

rho

Numeric. Tumor purity (fraction between 0 and 1).

C_i

Numeric. Integer copy number of the mutation.

Value

Numeric. The estimated cancer cell fraction (CCF), with Inf and -Inf values capped at 1 and 0.01, respectively.

Details

The formula is:
ccf = ((C_i * 2 / (mu * 100)) - ((1 - rho) * 2) - (rho * 2)) / (rho * (CN - 2))
If CCF is -Inf, returns 0.01; if Inf, returns 1; otherwise returns the computed value.

Examples

Calccf(CN = 4, mu = 100, rho = 0.6, C_i = 2)
#> [1] -1.666333