genesetdnds: genesetdnds

In im3sanger/dndscv: Poisson-based dN/dS models to quantify natural selection in somatic evolution

genesetdnds

Description

Function to estimate global dN/dS values for a gene set when using whole-exome data. Global dN/dS values for a set of genes can also be obtained using dndscv (gene_list argument), but that option estimates the trinucleotide mutation rates exclusively from the list of genes of interest. This may be prefereable in large datasets, but in small datasets, the genesetdnds option estimates global dN/dS values for a set of genes while using all genes in the exome to fit the substitution model. Usage: genesetdnds(dndsout, gene_list).

Usage

genesetdnds(dndsout, gene_list, sm = "192r_3w")

Arguments

dndsout	Output object from dndscv. To generate a valid input object for this function, use outmats=T when running dndscv.
gene_list	List of genes to restrict the analysis (gene set).
sm	Substitution model (precomputed models are available in the data directory)

Details

Martincorena I, et al. (2017) Universal patterns of selection in cancer and somatic tissues. Cell. 171(5):1029-1041.

Value

'genesetdnds' returns a list of objects:

globaldnds_geneset: Global dN/dS estimates in the gene set, including Wald CI95

globaldnds_rest: Global dN/dS estimates in all other genes, including Wald CI95

Author(s)

Inigo Martincorena (Wellcome Sanger Institute)

im3sanger/dndscv documentation built on Oct. 1, 2023, 1:05 p.m.