生物信息学QuantumClone软件使用

QuantumClone是根据等位基因频率VAF识别，考虑亚克隆基因型，识别肿瘤中的亚克隆的一个软件，其R packages网址为：
https://cran.r-project.org/web/packages/QuantumClone/
输入SNV_list格式如下：



今天自己用了一下，是这样处理的：

library(QuantumClone)
sim <- read.table("input.txt", header = T)
quantum <- data.frame(Sample = "Example_1", SampleName = "Timepoint_1", Chr = 3, Start = sim[,1], Depth = sim[,4] + sim[,5], Alt = sim[,5], Genotype = "AB")
Mutations <- list()
Mutations[[1]] <- quantum
Clustering_output <- QuantumClone(SNV_list = Mutations, FREEC_list = NULL, contamination = c(0, 0), nclone_range = 2, clone_priors = NULL, prior_weight = NULL, maxit = 1, preclustering = TRUE, simulated = TRUE, save_plot = TRUE, ncores = 1, output_directory = "Example")
write.table(Clustering_output$cluster, "quantum_out.txt", quote = F, row.names = F, col.names = F)