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SingleR-inc / SingleR

Clone of the Bioconductor repository for the SingleR package.
https://bioconductor.org/packages/devel/bioc/html/SingleR.html
GNU General Public License v3.0
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could not find function "CreateSinglerObject" #245

Closed coconutll closed 10 months ago

coconutll commented 11 months ago

library(SingleR) counts<-pbmc@assays$RNA@counts clusters<-pbmc@meta.data$seurat_clusters ann=pbmc@meta.data$orig.ident singler = CreateSinglerObject(counts, annot = ann, "pbmc", min.genes = 0, species = "Human", citation = "", ref.list = list(), normalize.gene.length = F, variable.genes = "de", fine.tune = F, do.signatures = T, clusters = clusters, do.main.types = T, reduce.file.size = T, numCores = 1)

and then

Error in CreateSinglerObject(counts, annot = ann, "pbmc", min.genes = 0, object 'CreateSinglerObject' not found

I'm sorry to bother you. After consulting the information, I found that it seems to be a version problem, I do not know where to download the package with this function, or what function can be replaced with this function in the current version. I'm looking forward to your response.

LTLA commented 11 months ago

CreateSingleRObject hasn't existed in the package for several years. I don't know what documentation you're following, but consider reading the instructions in the book.