callCN: Copy number call categories from ratio data

In SingerLab/gac: Genetic Analysis of Cells

Copy number call categories from ratio data

Description

Copy number call categories from ratio data

Usage

callCN(
  cnr,
  cbioportal = FALSE,
  hyper.amplification = TRUE,
  deletion.threshold = 0,
  loss.threshold = 1,
  base.ploidy = 2,
  gains.thresholds = c(3, 5),
  amplification.thresholds = c(6, 20)
)

Arguments

cnr	a cnr bundle
cbioportal	logical, weather to use the cBioPortal copy number call categories of -2, -1, 0, 1, 2 to denote deletion, loss, neutral, gain, amplificiation, respectively. Default is FALSE. If TRUE, hyper amplification calls will be joined with 2
hyper.amplification	logical, weather to call hyper amplifications where the number of copies exceeds the upper bound amplification threshold defaults to TRUE, and uses 20 as the default. Parameter is ignored if cBioPortal notation is TRUE
deletion.threshold	integer to use as locus deletion, default = 0
loss.threshold	number of copies to use as copy number loss, default = 1
base.ploidy	integer to denote base ploidy to use as Neutral
gains.thresholds	number of copies to use as copy number gains, default to a ower bound of 3 (+1 copy from 2N) and upper bound of 5 (+3 copies)
amplification.thresholds	number of copies to use as copy number amplification defaults to a lower bound of 6 (+4 copies) and upper bound of 20 (+18 copies)

Value

With default parameters, the function returns a matrix with copy number calls in the form of D, L, N, G, A and A2 from an genotype X matrix.

| CN | Call | cBioPortal Notation | |——:|: —- :|: —————– :| | 0 | D | -2 | | 1 | L | -1 | | 2 | N | 0 | | 3-5 | G | 1 | | 6-20 | A | 2 | | >20 | A2 | 2 |

Examples

data(cnr)

Xc <- callCN(cnr)
Xc <- callCN(cnr, hyper.amplification = FALSE)

Xp <- callCN(cnr, cbioportal = TRUE)

SingerLab/gac documentation built on Oct. 14, 2022, 4:09 a.m.