使用ArchR进行ATAC-seq测序遇到的问题

使用ArchR进行ATAC-seq测序遇到的问题

addDoubletScores

// An highlighted block
doubScores <- addDoubletScores(
  input = ArrowFiles,
  k = 10, #Refers to how many cells near a "pseudo-doublet" to count.
  knnMethod = "UMAP", #Refers to the embedding to use for nearest neighbor search with doublet projection.
  LSIMethod = 1
)

ERROR Found in addIterativeLSI

<simpleError in .logError(e, fn = “.LSIPartialMatrix”, info = “”, errorList = errorList, logFile = logFile): Exiting See Error Above>

解决方法

我遇到这个问题的原因是Matrix版本导致的，应为1.6-1.1，而相对应地seurat的版本也需要进行修改。

// An highlighted block

#重装Matrix:

remove.packages("Matrix")

remotes::install_version("Matrix", version = "1.6-1.1")

#重装Seurat

options(repos="https://mirrors.tuna.tsinghua.edu.cn/CRAN/") 

remove.packages('SeuratObject')
packageurl <- "https://cran.r-project.org/src/contrib/Archive/SeuratObject/SeuratObject_4.1.4.tar.gz" 
install.packages(packageurl, repos=NULL, type="source")

remove.packages('Seurat')
packageurl <- "https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz" 
install.packages(packageurl, repos=NULL, type="source")

参考来源：https://blog.csdn.net/weixin_64317226/article/details/134651916