【AUCell】单细胞基因集打分

最新推荐文章于 2024-04-21 07:28:08 发布

VIP文章 DerekRusso

最新推荐文章于 2024-04-21 07:28:08 发布

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分类专栏： gene set/signature scoring 文章标签： r语言

本文链接：https://blog.csdn.net/DerekRusso/article/details/124425485

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单细胞层次给基因集打分除了和GSVA等分析一样可以做富集以外，还可以通过cell marker gene set做亚群注释（需要注意细胞比例的问题，数量少的群体不行，可作辅助）。前面写过的scMetabolism包是给代谢通路打分，思路一样。

AUCell 是ranking-based，所以具体哪种标准化方法不重要，只要不影响每个细胞内基因表达量的排序就好。总的来讲，分为三步：

1，build the rankings

2，calculate the AUC

3，set the assignment threshold

安装R包

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

Biocmanager::install("AUCell")

# To support paralell execution:
BiocManager::install(c("doMC", "doRNG","doSNOW"))
# For the main example:
BiocManager::install(c("mixtools", "GEOquery", "SummarizedExperiment"))
# For the examples in the follow-up section of the tutorial:
BiocManager::install(c("DT", "plotly", "NMF", "d3heatmap", "shiny", "rbokeh",
                       "dynamicTreeCut","R2HTML","Rtsne", "zoo"))

load the scRNA expression matrix and gene set

# i.e. Reading from a text file
#exprMatrix <- read.table("myCountsMatrix.tsv")
#exprMatrix <- as.matrix(exprMatrix)

# or using an expression set
#exprMatrix <- exprs(myExpressionSet)




# (This may take a few minutes)
library(GEOquery)
attemptsLeft <- 20
while(attemptsLeft>0)
{
  geoFile <- tryCatch(getGEOSuppFiles("GSE60361", makeDirectory=FALSE), error=identity) 
  if(methods::is(geoFile,"error")) 
  {
    attemptsLeft <- attemptsLeft-1
    Sys.sleep(5)
  }
  else
    attemptsLeft <- 0
}

gzFile <- grep(".txt.gz", basename(rownames(geoFile)), fixed=TRUE, value=TRUE)
message(gzFile)
txtFile <- gsub(".gz", "", gzFile, fixed=TRUE)
message(txtFile)
gunzip(filename=gzFile, destname=txtFile, remove=TRUE)

library(data.table)
geoData <- fread(txtFile, sep="\t")
gene