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A two-way mixture Poisson model for the deconvolution of read-depth information and inferred the subclonal copy number of each target region, mutational cellular prevalence (MCP), subclone composition.
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README.md

README.md

CloneDeMix

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:

  1. install.packages("devtools")
  2. library(devtools)
  3. install_github("AshTai/CloneDeMix")

Example

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)

Contact information

Anshun Tai (daansh13@gmail.com) https://anshuntai.weebly.com

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