CloneDeMix: Decomposing the subclonal structure of tumors with two-way...

In AshTai/CloneDeMix: Clone deconvolution via DNA sequencing

Description

A R package for deconvoluting subclonal copy number and mutational cellular prevalence.

Usage

CloneDeMix(tumor, normal = NULL, threshold = 10^-5, iterC = 10^3,
  CNVstate = c(0:10), method = "aic")

Arguments

tumor	A G by N count matrix of tumor samples, where G is the gene number and N is the sample size.
normal	A vector of length s. It's DNA profile from the paired normal sample. If it's empty, the baseline is calculated from sample mean.
threshold	The threhold of convergence. Default is 10^-5.
CNVstate	A vector of considered copy number state.
method	The criteria for the final clone number.
iterationC	Maximum number of iterations. Default is 1000.

Value

A list is containing an estimated CNV matrix, MCP matrix, and the number of predicted clone number.

Author(s)

An-Shun Tai [e-mail]

Examples

data("ESCC_chr1")
res <- CloneDeMix(tumor=ESCC_chr1$tumor, normal=ESCC_chr1$normal)
head(res$CNV); head(res$MCP)

AshTai/CloneDeMix documentation built on May 28, 2019, 11:04 a.m.