calc.lst: Large-scale state transitions

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

Large-scale state transitions

Description

This function implements Popova's LST measure as described (Popova 2012, Cancer research) Popova's cutoffs: 15 LSTs in near-diploid, 20 in near-tetraploid. 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.lst(
  seg,
  chrominfo = chrominfo.snp6,
  nA = 7,
  check.names = FALSE,
  return.loc = FALSE,
  chr.arm = "no"
)

Arguments

seg	seg must be an ASCAT output object, in DNAcopy format. Requires the following columns in the given order: "SampleID", "Chromosome", "Start", "End", "nProbes", "totalCN", "nA", "nB", "Ploidy" and "AberrantCellFraction". Column "nProbes" is not used here and can be set to NA.
nA	is the column where copy number of A allele is found. This needs to be set to 7, because of the columns are referenced by position according to the required column order of seg.

Author(s)

Nicolai Juul Birkbak, [e-mail]

References

Popova, T., Manié, E., Rieunier, G., Caux-Moncoutier, V., Tirapo, C., Dubois, T., ... Stern, M. H. (2012). Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. Cancer Research, 72(21), 5454–5462. https://doi.org/10.1158/0008-5472.CAN-12-1470

Examples

res <- calc.lst(seg)

Nik-Zainal-Group/signature.tools.lib documentation built on Jan. 28, 2024, 5:17 a.m.