copynumber

copynumber 是一个功能强大拷贝数分析工具，这里仅限于自己用的的部分功能，看到可用hg38版本，就尝试运行了一下，识别CNV break points。

remotes::install_github("ShixiangWang/copynumber")
library('sequenza')
data("lymphoma")
sub.lymphoma <- subsetData(lymphoma,sample=1:3)
wins.lymph <- winsorize(sub.lymphoma)

#单个样本
pcf.segments <- pcf(data=wins.lymph,gamma=12,Y=sub.lymphoma, assembly = "hg38")

pcf.segments <- pcf(data=wins.lymph,gamma=12,Y=sub.lymphoma, assembly = "hg19")


##多个样本：
pcf.segments11 <- multipcf(data= wins1,gamma=12,Y=dat1, assembly = "hg38")
pcf.segments22 <- multipcf(data= wins1,gamma=12,Y=dat2, assembly = "hg38")