callDNA_CN: call copy numbers out of CNR data

In SingerLab/gac: Genetic Analysis of Cells

call copy numbers out of CNR data

Description

call copy numbers out of CNR data

Usage

callDNA_CN(
  cnr,
  cbioportal = FALSE,
  deletion.threshold = -0.5,
  loss.threshold = -0.1,
  gains.threshold = 0.1,
  amplification.threshold = 1
)

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
deletion.threshold	integer to use as locus deletion, default -0.5
loss.threshold	copy number ratio to use as copy number loss, default -0.1
gains.threshold	copy number ratio to use as copy number gains, default 0.1
amplification.threshold	copy number ratio to use as copy number amplification default 1

Value

returns a matrix with copy number calls in the form of D, L, N, G, A1 and A2 from an X matrix

| CN | Call | cBioPortal Notation | |———-:|: —- :|: —————– :| | -0.50 | D | -2 | | -0.10 | L | -1 | |-0.1 - 0.1 | N | 0 | | 0.1 - 1.0 | G | 1 | | >1.0 | A | 2 |

Examples

data(cnr)

Xc <- callDNA_CN(cnr)

Xp <- callDNA_CN(cnr, cbioportal = TRUE)

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