dot-test_NB_model: Runs negative binomial regression and likelihood ratio test
In reimandlab/RM2: Regression Models For Localised Mutations

.test_NB_model

R Documentation

Runs negative binomial regression and likelihood ratio test

Description

Runs negative binomial regression and likelihood ratio test

Usage

.test_NB_model(dfr, mut_type, n_min_mut = 100, test_cofactor = F)

Arguments

`dfr`	Data frame generated from maf_to_dfr that contains mutation and trinucleotide counts for each quadnucleotide context + indel
`mut_type`	Character corresponding to total mutations or name of subclass
`n_min_mut`	Integer (default 100) representing the minimum number of mutations required to run test
`test_cofactor`	Boolean indicating whether to analyze cofactor

Value

Data frame containing the results of the regression with the following columns: mut_type, pp, this_coef, obs_mut, exp_mut, exp_mut_lo, exp_mut_hi, fc, pp_cofac, this_coef_cofac

mut_type: A string identifying the mutation class
pp: The p-value from the likelihood ratio test
this_coef: The coefficient from is_site
obs_mut: The total number of observed mutations of that class
exp_mut: The expected number of mutations determined by the model
exp_mut_lo: Lower bound of 95% confidence interval
exp_mut_hi: Upper bound of 95% confidence interval
fc: Observed mutations divided by expected mutations
pp_cofac: The p-value from the likelihood ratio test of site:cofactor interaction
this_coef_cofac: The coefficient from the site:cofactor interaction term