MutSet: MutSet class

In bioinform/ecTMB: Esitmation and Classification of TMB

Description

MutSet class

Usage

MutSet

Format

An R6Class object.

Value

Object of class MutSet

Slots

mut

table from MAF

gid

list of gene id for analysis

exome

table contains all possible mutations

exomeGene

table contains all posiible mutations for each gene.

covar

table contains covariates for each gene

mutContext

The context of 96 mutations

samples

data.frame store sample info. if BED colunm is specified, the background process will be using the regions limited to bed file.

incosistantAnno

Variants with incosistant gene annotation from GSMuta reference data .

new()

Create a MutSet

nonsilent()

Get nonsilent mutations table

silent()

Get silent mutations table

nc()

Get noncoding mutations table

Examples

## Not run: 
MutSet$new()

## End(Not run)

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