fit_model: fit_model

In bioinform/ecTMB: Esitmation and Classification of TMB

Description

fit background model with negative-binomial regression

Usage

fit_model(Data, MRtriProb, method = "NB", cores = 1, bs.type = "all",
  mut.nonsil = FALSE, nonsil.fraction = 0.6)

Arguments

Data	mutSet object
MRtriProb	output from get_bg_MRtri
method	Either NB or Poisson
cores	Number of parallel core to be used
bs.type	Either 'all' or nonsil. When all is specificed, all mutation per Mb will be used as sample specific background mutation (TMB). When nonsil is specified, non-synonymous mutation per Mb will be used as sample specific background mutation (TMB).
mut.nonsil	A boolen. If TRUE, non-synonymous mutation will be used for background mutation modeling during training.
nonsil.fraction	Default is 0.6. The percentage of genes whose non-synonymous mutation will be used.

Value

A vector mutation count for 96 trinucleotide context

Examples

## Not run: 
fit_model2(Data)

## End(Not run)

bioinform/ecTMB documentation built on Aug. 29, 2021, 6:17 p.m.