SingleR ref<- HumanPrimaryCellAtlasData()报错

2023-11-08 16:25:22 浏览数 (2)

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)

0 人点赞