calc.ai: Number of Telomeric Allelic Imbalances

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

Number of Telomeric Allelic Imbalances

Description

This function computes the number of Telomeric AI (NtAI). Implementation of Nicolai Juul Birkbak, [e-mail] (2014-07-02). This functions generally rely on ASCAT or similarly processed copy number data, in a matrix format with at least the follwing columns in this exact order: "SampleID", "Chromosome", "Start", "End", "nProbes", "totalCN", "nA", "nB", "Ploidy" and "AberrantCellFraction". NOTE: currently the chrominfo data refers to hg19, while hg38 is not yet supported.

Usage

calc.ai(
  seg,
  chrominfo = chrominfo,
  min.size = 0,
  min.probes = 500,
  cont = 0,
  check.names = FALSE,
  ploidyByChromosome = TRUE,
  return.loc = FALSE,
  shrink = TRUE
)

Arguments

seg	input data frame. Segmented output in the form of an ASCAT out matrix, which also includes ploidy and contamination. Total CN in column 6, nA in column 7, nB in column 8, ploidy in column 9, and contamination in column 10. Requires the following columns in the given order: "SampleID", "Chromosome", "Start", "End", "nProbes", "totalCN", "nA", "nB", "Ploidy" and "AberrantCellFraction".
chrominfo	data frame that contains necessary chromosome information. No need to specify this for human chromosomes, it will be loaded internally. A 3 column matrix with information about the chromosomes: chromosome name, chromosome length, centromere location.
min.size	minimum size of segments
min.probes	minimum number of probes in segments (I use 500 for the 900,000 probe SNP6, then scale down)
cont	contamination threshold. By default set at 0 to ignore contamination
check.names	check and potentially fix if there are duplicated samples. Any duplicates shall be re-named. Works by combining sample names with ploidy and SNP file name (which for this to work must be in column 11). Then looks for individual sample names which matches multiple original SNP files.
shrink	joins segments of identical allelic copy number

Author(s)

Nicolai Juul Birkbak, [e-mail]

References

Birkbak, N. J., Wang, Z. C., Kim, J.-Y., Eklund, A. C., Li, Q., Tian, R., ... Richardson, A. L. (2012). Telomeric Allelic Imbalance Indicates Defective DNA Repair and Sensitivity to DNA-Damaging Agents. Cancer Discovery, 2(4), 366–375. https://doi.org/10.1158/2159-8290.CD-11-0206

Examples

res <- calc.ai(seg)

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.