geneci: geneci

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

geneci

Description

Function to calculate confidence intervals for dN/dS values per gene under the dNdScv model using profile likelihood. To generate a valid dndsout input object for this function, use outmats=T when running dndscv.

Usage

geneci(dndsout, gene_list = NULL, level = 0.95)

Arguments

dndsout	Output object from dndscv.
gene_list	List of genes to restrict the analysis (by default, all genes in dndsout will be analysed)
level	Confidence level desired [default = 0.95]

Details

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

Value

ci: Dataframe with the confidence intervals for dN/dS ratios per gene under the dNdScv model.

Author(s)

Inigo Martincorena (Wellcome Sanger Institute)

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