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R toolkit for single cell genomics
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Joining Layers after SCTransform #8558

Open chungsai opened 8 months ago

chungsai commented 8 months ago

Hi, I have a merged object that I did SCTransform on,

merged_samples <- merge(seur_norm_list[[1]], c(seur_norm_list[[2]], seur_norm_list[[3]], seur_norm_list[[4]] ), # add.cell.ids = names(seur_raw_list), project = input_type, merge.data = TRUE)

merged_samples <- SCTransform(merged_samples )

but after trying

merged_samples <- JoinLayers(merged_samples) merged_samples <- JoinLayers(merged_samples, layers= 'SCT')

I get the error. Error in UseMethod(generic = "JoinLayers", object = object) : no applicable method for 'JoinLayers' applied to an object of class "c('SCTAssay', 'Assay', 'KeyMixin')"

Same error occurs even after IntegrateLayers.

I want to join layers get sce = GetAssayData(merged_samples, 'SCT')

This problem doesn't occur when I run the traditional

list <- lapply(X = raw, FUN = function(x) { x <- NormalizeData(x) x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 2000) })

and then merge using the same code then join layers.

session_info() ─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.3.2 (2023-10-31) os macOS Ventura 13.0 system aarch64, darwin20 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/Toronto date 2024-02-29 rstudio 2023.12.1+402 Ocean Storm (desktop) pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

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[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

saketkc commented 8 months ago

Hi @chungsai, what is the goal here? SCTransform is a v3 assay so there are no layers.

denvercal1234GitHub commented 3 months ago

Hi @saketkc,

I also encountered the error below for my Seurat Object. I want to join layers of RNA assay 

Tonsil_IndividualDatasetMERGED[["RNA"]] <- SeuratObject::JoinLayers(Tonsil_IndividualDatasetMERGED[["RNA"]])

Error in UseMethod(generic = "JoinLayers", object = object) : 
  no applicable method for 'JoinLayers' applied to an object of class "c('Assay', 'KeyMixin')"
Layers(Tonsil_IndividualDatasetMERGED)
[1] "counts"     "data"       "scale.data"
WilliamMWei commented 1 month ago

Hi @saketkc,

I also encountered the error below for my Seurat Object. I want to join layers of RNA assay

Tonsil_IndividualDatasetMERGED[["RNA"]] <- SeuratObject::JoinLayers(Tonsil_IndividualDatasetMERGED[["RNA"]])

Error in UseMethod(generic = "JoinLayers", object = object) : 
  no applicable method for 'JoinLayers' applied to an object of class "c('Assay', 'KeyMixin')"
Layers(Tonsil_IndividualDatasetMERGED)
[1] "counts"     "data"       "scale.data"

Samee problem here :/