README.md

AneuploidyScore

The point of this package is to calculate the Aneuploidy Score for a chromosomal arm SCNA/aneuploidy (CAA) as detailed in the following two papers:

Installation

Install using

devtools::install_github("quevedor2/aneuploidy_score", ref='master') # Latest stable build
devtools::install_github("quevedor2/aneuploidy_score", ref='dev') # Development branch

A guide for how to use the package can be found at inst/rmd/demo_guide.html

Details of Aneuploidy Score/CAA

Defintions:

AS and CAAs are calculated two different ways:

Basic Usage

To have some data to work with, the CCLE 639-V cell line seg file is included in the package, as well as cytobands downloaded from UCSC table browser for:

library(AneuploidyScore)
data("seg")
data("ucsc.hg19.cytoband")

Clump the cytobands into p-arm, q-arm and centromere segments, then split by chromosome:

cytoarm <- cytobandToArm(ucsc.hg19.cytoband)

Estimate the ploidy of your individual sample (this method uses the weighted-mean approach):

tcn_col <- 'TCN'
wgd_ploidy <- checkIfWGD(seg, tcn_col = tcn_col, threshold = 0.5,
                         wgd_gf = 0.5, ploidy_method = 'wmean')

Using the estimated ploidy, identify the classification of Loss/Neutral/Gain (-1/0/1) for each CN segment (segCNclass) or the Cohen-Sharir's weighted-median chromosome arm (armCNclass).

threshold <- 0.5
seg_caa <- getCAA(seg, cytoarm, tcn_col=tcn_col, classifyCN=TRUE,
                  ploidy=wgd_ploidy['ploidy'], threshold=threshold)

Reduce the CN-segment specific GRangesList object down to a simplified chromosome-arm representation and calculate the aneuploidy score:

caa <- reduceArms(seg_caa, caa_method=c('arm', 'seg'),
                  arm_ids = c('p', 'q'))
AS <- colSums(abs(caa), na.rm = TRUE)


quevedor2/aneuploidy_score documentation built on Feb. 26, 2021, 12:13 p.m.