R/get_Aneuploidy_score.R
get_Aneuploidy_score.Rd
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.
get_Aneuploidy_score( data, ploidy_df = NULL, genome_build = "hg19", rm_black_arms = FALSE )
data | a CopyNumber object or a |
---|---|
ploidy_df | default is |
genome_build | genome build version, should be 'hg19', 'hg38', 'mm9' or 'mm10'. |
rm_black_arms | if |
A data.frame
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.
# 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