runCIN: Compute chromosomal instability
In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

runCIN

R Documentation

Compute chromosomal instability

Description

Computes chromosomal instability scores based on copy number variation results according to Drews et al., 2022. Requires the results of runCNV(). See details for more.

Usage

runCIN(
  object,
  bin_size = 1e+06,
  window_k = 10,
  noise = 0.035,
  gene_pos_df = SPATA2::gene_pos_df,
  chrom_regions_df = SPATA2::cnv_regions_df,
  coverage_model = SPATA2::coverage_model,
  verbose = NULL
)

Arguments

`object`	An object of class `SPATA2` or, in case of S4 generics, objects of classes for which a method has been defined.
`bin_size`	The size used for the chromosomal binning. Defaults 1.000.000 base pairs.
`window_k`	Given to `window.k` of `imputeTS::na_ma`.
`noise`	Numeric value. Sets the level of noise to add.
`gene_pos_df`	Data.frame defining the positions of genes on the chromosomes.
`chrom_regions_df`	Data.frame defining the chromosomal regions.
`coverage_model`	A formula.
`verbose`	Logical. If `TRUE`, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Details

Adds a total of 18 new numeric variables to the meta data.frame.

CX1, CX2, CX3, ..., CX17: Chromosomal instability scores as described in the paper referenced below.
ploidy: Quantification of abnormal ploidy.

Adding these variables is forced! Existing variable with equal names will be overwritten!

Note

Requires the packages CINSignatureQuantification and imputeTS to be installed.

References

Drews, R.M., Hernando, B., Tarabichi, M. et al. A pan-cancer compendium of chromosomal instability. Nature 606, 976–983 (2022). https://doi.org/10.1038/s41586-022-04789-9

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.