tcgaCompare {maftools} | R Documentation

## Compare mutation load against TCGA cohorts

### Description

Compares mutation load in input MAF against all of 33 TCGA cohorts derived from MC3 project.

### Usage

    tcgaCompare(
      maf,
      capture_size = NULL,
      tcga_capture_size = 35.8,
      cohortName = NULL,
      tcga_cohorts = NULL,
      primarySite = FALSE,
      col = c("gray70", "black"),
      bg_col = c("#EDF8B1", "#2C7FB8"),
      medianCol = "red",
      decreasing = FALSE,
      logscale = TRUE,
      rm_hyper = FALSE,
      rm_zero = TRUE,
      cohortFontSize = 0.8,
      axisFontSize = 0.8
    )

### Arguments

`maf` | `MAF` object(s) generated by `read.maf`
`capture_size` | capture size for input MAF in MBs. Default NULL. If provided plot will be scaled to mutations per mb. TCGA capture size is assumed to be 35.8 mb.
`tcga_capture_size` | capture size for TCGA cohort in MB. Default 35.8. Do NOT change. See details for more information.
`cohortName` | name for the input MAF cohort. Default "Input"
`tcga_cohorts` | restrict tcga data to these cohorts.
`primarySite` | If TRUE uses primary site of cancer as labels instead of TCGA project IDs. Default FALSE.
`col` | color vector for length 2 TCGA cohorts and input MAF cohort. Default gray70 and black.
`bg_col` | background color. Default'#EDF8B1', '#2C7FB8'
`medianCol` | color for median line. Default red.
`decreasing` | Default FALSE. Cohorts are arranged in increasing mutation burden.
`logscale` | Default TRUE
`rm_hyper` | Remove hyper mutated samples (outliers)? Default FALSE
`rm_zero` | Remove samples with zero mutations? Default TRUE
`cohortFontSize` | Default 0.8
`axisFontSize` | Default 0.8

### Details

Tumor mutation burden for TCGA cohorts is obtained from TCGA MC3 study. For consistency TMB is estimated by restricting variants within Agilent Sureselect capture kit of size 35.8 MB.

### Value

data.table with median mutations per cohort

### Source

TCGA MC3 file was obtained from https://api.gdc.cancer.gov/data/1c8cfe5f-e52d-41ba-94da-f15ea1337efc. See TCGAmutations R package for more details. Further downstream script to estimate TMB for each sample can be found in ‘inst/scripts/estimate_tcga_tmb.R’

### References

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines Kyle Ellrott, Matthew H. Bailey, Gordon Saksena, et. al. Cell Syst. 2018 Mar 28; 6(3): 271–281.e7. https://doi.org/10.1016/j.cels.2018.03.002

### Examples

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

[Package maftools version 2.10.05 Index]