SingleR ref<- HumanPrimaryCellAtlasData()报错

代码语言：javascript复制

library(celldex)
library(SingleR)
library(BiocParallel)
ref<- HumanPrimaryCellAtlasData()
Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) : 
  Invalid Cache: sqlite file
  Hub has not been added to cache
  Run again with 'localHub=FALSE'
In addition: Warning message:
HumanPrimaryCellAtlasData不再有用。
请用'celldex::HumanPrimaryCellAtlasData'。
见help("Deprecated") 

解决办法：

下载注释数据库（我的保存至F:sxjns hdanxibaosingleR zhushiku），复制一份到当前工作目录，加载即可使用

代码语言：javascript复制

library(celldex)
library(SingleR)
library(BiocParallel)
refdata <- get(load("HumanPrimaryCellAtlas_hpca.se_human.RData"))
scRNA = pbmc
pred.scRNA <- SingleR(test = scRNA@assays$RNA$data, 
                      ref = refdata,
                      labels = refdata$label.main, 
                      clusters = scRNA@active.ident)

r语言 生物基因

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