tmb: Estimate Tumor Mutation Burden

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Estimates Tumor Mutation Burden in terms of per megabases

Usage

tmb(maf, captureSize = 50, logScale = TRUE)

Arguments

maf	maf MAF object
captureSize	capture size for input MAF in MBs. Default 50MB.
logScale	Default TRUE. For plotting purpose only.

Value

data.table with TMB for every sample

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
tmb(maf = laml)

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.447s elapsed (0.395s cpu) 
     Tumor_Sample_Barcode total total_perMB total_perMB_log
  1:         TCGA-AB-2903     0        0.00            -Inf
  2:         TCGA-AB-2823     1        0.02      -1.6989700
  3:         TCGA-AB-2834     1        0.02      -1.6989700
  4:         TCGA-AB-2840     1        0.02      -1.6989700
  5:         TCGA-AB-2842     1        0.02      -1.6989700
 ---                                                       
189:         TCGA-AB-2972    20        0.40      -0.3979400
190:         TCGA-AB-3002    21        0.42      -0.3767507
191:         TCGA-AB-2959    23        0.46      -0.3372422
192:         TCGA-AB-2807    25        0.50      -0.3010300
193:         TCGA-AB-3009    34        0.68      -0.1674911

maftools documentation built on Feb. 6, 2021, 2 a.m.