ecTMB is a powerful and flexible statistical framework for TMB estimation and classification. It uses an explicit background mutation mdoel for more robust and consistent TMB prediction. The backgournd mutation model takes account of unknown as well as known mutational heterogeneous factors, including tri-nucleotide context, sample mutational burden, gene expression level and replication timing by utilization of a Bayesian framework. The discovery of three TMB-based subtypes, including one novel subtype TMB-extreme, enable ecTMB to classify samples to biological and clinically relavent TMB subtypes.
Dependency
Installation
Example Usage
License
ecTMB has been sucessfully tested on Intel(R) Xeon(R) CPU E5-2680 v4 Machine with 28 cores.
ecTMB import following R packages: ggplot2, limma, reshape2, dplyr, R6, MASS, GenomicRanges, data.table, parallel, mixtools
ecTMB also depends on bedtools 2.27.1 and R = 3.5.1
You can install these packages using anaconda/miniconda :
conda install bedtools=2.27.1 r=3.5.1
Then you can export the conda paths as:
export PATH="/PATH/TO/CONDA/bin:$PATH"
export LD_LIBRARY_PATH="/PATH/TO/CONDA/lib:$LD_LIBRARY_PATH"
install.packages("devtools")
library(devtools);
devtools::install_github("bioinform/ecTMB");
#Example file download from URL: https://www.dropbox.com/s/knpgl73samhdtvg/ecTMB_data.tar.gz?dl=1
URL = "https://github.com/bioinform/ecTMB/releases/download/v0.1.0/ecTMB_data.tar.gz"
download.file(URL,destfile = "ecTMB.example.tar.gz")
untar("./ecTMB.example.tar.gz")
URL_ref = "https://api.gdc.cancer.gov/data/254f697d-310d-4d7d-a27b-27fbf767a834"
download.file(URL_ref,destfile = "GRCh38.d1.vd1.fa.tar.gz")
untar("./GRCh38.d1.vd1.fa.tar.gz")
library(ecTMB)
load("./ecTMB_data/example/UCEC.rda")
extdataDir = "./ecTMB_data/references"
exomef = file.path(extdataDir, "exome_hg38_vep.Rdata" ) #### hg38 exome file
covarf = file.path(extdataDir,"gene.covar.txt") ### gene properties
mutContextf = file.path(extdataDir,"mutation_context_96.txt" ) ### 96 mutation contexts
TST170_panel = file.path(extdataDir,"TST170_DNA_targets_hg38.bed" ) ### 96 mutation contexts
ref = file.path("./","GRCh38.d1.vd1.fa" )
* **Set random 70% as training and rest as test set**
set.seed(1002200) SampleID_all = UCEC_cli$sample SampleID_train = sample(SampleID_all, size = round(2 * length(SampleID_all)/3), replace = F) SampleID_test = SampleID_all[!SampleID_all %in% SampleID_train]
* **Generate train and test data object**
trainData = UCEC_mafs[UCEC_mafs$Tumor_Sample_Barcode %in% as.character(SampleID_train),] trainset = readData(trainData, exomef, covarf, mutContextf, ref)
sample = data.frame(SampleID = SampleID_test, BED = TST170_panel, stringsAsFactors = FALSE) testData = UCEC_mafs[UCEC_mafs$Tumor_Sample_Barcode %in% as.character(SampleID_test),] testset_panel = readData(testData, exomef, covarf, mutContextf, ref, samplef = sample) testset_WES = readData(testData, exomef, covarf, mutContextf, ref) ## to calculate WES-TMB for test samples
* **Background mutation model training**
---
**NOTE**
This step takes up to ~12 mins when 24 parallel processes are used. You can skip
and use the pre-loaded parameters defined from training data set.
---
MRtriProb_train= getBgMRtri(trainset) trainedModel = fit_model(trainset, MRtriProb_train, cores = 24)
* **Predict TMB for TST170 panel**
TMBs = pred_TMB(testset_panel, WES = testset_WES, cores = 1, params = trainedModel, mut.nonsil = T, gid_nonsil_p = trainset$get_nonsil_passengers(0.95))
library(dplyr) library(ggplot2)
TMBs %>% melt(id.vars = c("sample","WES_TMB")) %>% ggplot( aes(x = WES_TMB, y = value, color = factor(variable, levels = c("ecTMB_panel_TMB", "count_panel_TMB")), group = factor(variable))) + geom_point() + geom_abline(slope = 1, intercept = 0) + scale_x_continuous(trans='log2') + scale_y_continuous(trans='log2') + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + theme(legend.title=element_blank()) + labs(x = "TMB defined by WES", y = sprintf("Predicted TMB from panel: TST170"))
* **Classify sample to 3 subtypes**
Subtypes = assignClass(TMBs$ecTMB_panel_TMB, prior = GMM_params)
## License
ecTMB is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.