This is an R package designed for inferring subclonal structure of tumors on copy number aberrations.
To install this package, please copy and paste following codes into your R session:
library(CloneDeMix) data("ESCC_chr1") # ESCC_chr1$tumor is a G by N count matrix of tumor samples, where G is the number of loci and N is the sample size. # ESCC_chr1$normal is a DNA count vector of a normal sample. res <- CloneDeMix(tumor=ESCC_chr1$tumor, normal=ESCC_chr1$normal,threshold = 10^-5, iterC = 10^3, CNVstate = c(0:10), method = "aic") head(res$CNV); head(res$MCP)