get_Aneuploidy_score {sigminer}

Get Aneuploidy Score from Copy Number Profile

Description

This implements a Cohen-Sharir method (see reference) like "Aneuploidy Score" computation. You can read the source code to see how it works. Basically, it follows the logic of Cohen-Sharir method but with some difference in detail implementation. Their results should be counterpart, but with no data validation for now. Please raise an issue if you find problem/bugs in this function.

Usage

get_Aneuploidy_score(
  data,
  ploidy_df = NULL,
  genome_build = "hg19",
  rm_black_arms = FALSE
)

Arguments

data

a CopyNumber object or a data.frame containing at least 'chromosome', 'start', 'end', 'segVal', 'sample' these columns.

ploidy_df

default is NULL, compute ploidy by segment-size weighted copy number aross autosome, see get_cn_ploidy. You can also provide a data.frame with 'sample' and 'ploidy' columns.

genome_build

genome build version, should be 'hg19', 'hg38', 'mm9' or 'mm10'.

rm_black_arms

if TRUE, remove short arms of chr13/14/15/21/22 from calculation as documented in reference #3.

Value

A data.frame

References

• Cohen-Sharir, Y., McFarland, J. M., Abdusamad, M., Marquis, C., Bernhard, S. V., Kazachkova, M., ... & Ben-David, U. (2021). Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition. Nature, 1-6.

• Logic reference: https://github.com/quevedor2/aneuploidy_score/.

• Taylor, Alison M., et al. "Genomic and functional approaches to understanding cancer aneuploidy." Cancer cell 33.4 (2018): 676-689.

Examples

# Load copy number object
load(system.file("extdata", "toy_copynumber.RData",
  package = "sigminer", mustWork = TRUE
))

df <- get_Aneuploidy_score(cn)
df

df2 <- get_Aneuploidy_score(cn@data)
df2

df3 <- get_Aneuploidy_score(cn@data,
  ploidy_df = get_cn_ploidy(cn@data)
)
df3