compare_pangenomes: compare_pangenomes

In gtonkinhill/panstripe: Pangenome Plots

compare_pangenomes

Description

Compares the coefficients between two pangenomes datasets by including interaction terms in the GLM.

Usage

compare_pangenomes(
  fitA,
  fitB,
  family = "Tweedie",
  intercept = FALSE,
  modeldisp = TRUE,
  ci_type = "perc",
  conf = 0.95,
  nboot = 100,
  boot_pvalue = FALSE
)

Arguments

fitA	a 'panfit' object generated by the 'panstripe' function
fitB	a 'panfit' object generated by the 'panstripe' function
family	the family used by glm. One of 'Tweedie', 'Poisson', 'Gamma' or 'Gaussian'. (default='Tweedie')
intercept	whether or not to include an intercept term in the GLM (default=FALSE). Adding an intercept can increase the robustness of the algorithm to errors at higher branches of the phylogeny at the expense of less sensitivity.
modeldisp	whether or not to model the dispersion as a function of the covariates of interest if using a Tweedie family (default=TRUE)
ci_type	the method used to calculate the bootstrap CI (default='perc'). See boot.ci for more details.
conf	A scalar indicating the confidence level of the required intervals (default=0.95)
nboot	the number of bootstrap replicates to perform (default=100)
boot_pvalue	whether or not to calculate bootstrap p-values (default=FALSE)

Value

a list containing a summary of the comparison and the resulting 'glm' model object

Examples

simA <- simulate_pan(rate=1e-4, ngenomes = 200, mean_trans_size=3, fp_error_rate=1)
simB <- simulate_pan(rate=1e-3, ngenomes = 200, mean_trans_size=3, fp_error_rate=1)
fitA <- panstripe(simA$pa, simA$tree, nboot=0)
fitA$summary
fitB <- panstripe(simB$pa, simB$tree, nboot=0)
fitB$summary
comp <- compare_pangenomes(fitA, fitB, nboot=10)
comp$summary

gtonkinhill/panstripe documentation built on Feb. 27, 2025, 9:01 p.m.