cbioportal_copy_number_states: 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

cbioportal_copy_number_states(cnr, base.ploidy = 2, cbioportal = FALSE, ...)

Arguments

cnr	a cnr bundle
base.ploidy	sample base ploidy e.g. 2, 4, 8. Default is 2
cbioportal	logical, weather to use the cBioPortal copy number call categories of -2, -1, 0, +1, +2 to denote deletion, loss, neutral or base ploidy, gain, amplificiation, respectively. Default is FALSE. We added one extra category '+4' representing high amplifications equivalent to a locus having with >20 copies (log2 Ratio > 2.16).
...	Optional parameters passed down to cbioportal_states_from_log2_ratio or cbioportal_states_from_integer_cn. These are deletion.threshold, loss.threshold, gains.threshold, amplification.thresholds. amplification.thresholds can have one value e.g. 9. In this case, all copy numbers >= to 9 will be considered amplifications, and will skip the high amplification call. By default we pass two values, c(9, 20) for integer copy number, and 0.8 and 2.16 for log2 Ratio data common in bulk DNA.

Value

Function returns a a list with two matrices with copy number calls, one for bins, and one for genes. Calls are interpreted as deletion, loss, (ploidy)N, gain, amplification, high_amplicifation, from an genotype X matrix. Default thresholds are described below.

Thresholds are chosen based on the cnr$bulk argument. If bulk = FALSE, integer copy number thresholds are applied. If bulk = FALSE, log2 ratio thresholds are applied.

For integer copy number data thresholds are:

| CN | Call | cBioPortal Notation | |——+——————–+———————| | 0 | deletion | -2 | | 1 | loss | -1 | | 2 | (ploidy)N | 0 | | 3-8 | gain | 1 | | 9-20 | amplification | 2 | | >20 | high_amplicifation | 4 |

For bulk DNA log2 Ratio data thresholds are:

| log2(Ratio) | Call | cBioPortal Notation | |————-+——————–+———————| | -1.2 | deletion | -2 | | -0.6 | loss | -1 | | -0.6, +0.4 | (ploidy)N | 0 | | 0.4-0.8 | gain | 1 | | 0.8-2.16 | amplification | 2 | | >2.16 | high_amplicifation | 4 |

References

Thresholds for DNA were chosen from Mina et al. (2020) PMID:32989323

Examples

data(cnr)

Xc <- cbioportal_copy_number_states(cnr)

Xp <- cbioportal_copy_number_states(cnr, cbioportal = TRUE)

SingerLab/gac documentation built on March 23, 2024, 5:15 a.m.