callCN: Copy number call categories from ratio data

View source: R/callCN.R

callCNR Documentation

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.