fitlnpbin: fitlnpbin

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

fitlnpbin

Description

Function to fit a Lognormal-Poisson model to estimate overdispersion on synonymous changes for sitednds and codondnds.

Usage

fitlnpbin(
  nvec,
  rvec,
  level = 0.95,
  theta_option = "conservative",
  numbins = 10000
)

Arguments

nvec	Vector of observed counts of mutations per site.
rvec	Vector of expected counts of mutations per site.
level	Confidence level desired for the confidence interval of the overdispersion parameter [defaul=0.95]
theta_option	2 options: "mle" (uses the MLE of the overdispersion parameter) or "conservative" (uses the conservative bound of the CI95). Values other than "mle" will lead to the conservative option [default="conservative"]
numbins	Number of bins to discretise the rvec vector [default=1e4]. This enables fast execution of the LNP model in datasets of arbitrarily any size.

Value

'fitlnpbin' returns the maximum likelihood estimate and confidence intervals of the "sig" overdispersion parameter of the LNP model:

Author(s)

Inigo Martincorena (Wellcome Sanger Institute)

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