Provide text and graphical output for Tumor Mutational Burden (TMB) quantification

This function reads in input a list (or a list of lists), with sample name, filter description, sn object containing sequencing design and an object containing variants. It quantifies TMB based on these variants and generates in output a text file containing TMB values and a pdf file with a barplot visualization.

applyTMB(inputForTMB, assembly)

Arguments

inputForTMB	a list of lists with the following elements: sample name, filter description, design and a CollapsedVCF or data.frame object containing somatic variants
assembly	human genome assembly: hg19 or hg38

Value

Returns a data.frame with sample, filter, sequencing size, total number of mutations and number of mutations per megabase.

Author

Laura Fancello

Examples

## Read vcf
vcf_files <- list(Horizon5="Horizon5_ExamplePanel.vcf", 
                  HorizonFFPEmild="HorizonFFPEmild_ExamplePanel.vcf")
vcf_files <- lapply(vcf_files
                    , function(x) system.file("extdata", x, package = "TMBleR", mustWork = TRUE))
vcfs <- readVcfFiles(vcfFiles = vcf_files , assembly = "hg19")
#> Validate VCF input:
#> $Horizon5
#> $Horizon5$warnings
#> [1] "line 141: The VCF file contains 2 samples. Only the first (1_20170317_01_i01_0_horizon_5) will be used"            
#> [2] "line 142: AF is described both in FORMAT and in INFO of this and possibly other variants. FORMAT's AF will be used"
#> 
#> $Horizon5$errors
#> NULL
#> 
#> 
#> $HorizonFFPEmild
#> $HorizonFFPEmild$warnings
#> [1] "line 141: The VCF file contains 2 samples. Only the first (2_20170317_01_i01_0_horizon_ffpe_mild) will be used"    
#> [2] "line 142: AF is described both in FORMAT and in INFO of this and possibly other variants. FORMAT's AF will be used"
#> 
#> $HorizonFFPEmild$errors
#> NULL
#> 
#> 
#> Warnings and Errors exported to 'validator_check' variable

## Read design
design <- readDesign(system.file("extdata"
, "ExamplePanel_GeneIDs.txt"
, package = "TMBleR"
, mustWork = TRUE)
, assembly = "hg19"
, ids = "entrezgene_id")
#> Cache found

## Prepare data for TMB quantification, formatting it as required by the 
## applyTMB() function. While this is done automatically within the 
## applyFilters() function, on a non filtered vcf we need to use the function
## here described to get the correct format
vcfs_nonfiltered <- applyFilters(vcfs = vcfs, 
                                design = design,
                                assembly = "hg19")
                                    
## Perform TMB quantification
TMB_res=applyTMB(inputForTMB = vcfs_nonfiltered, assembly = "hg19")