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single cell RNA seq integration(Error in UseMethod(generic = "as.sparse", object = x))

enter image description here enter image description here

I don't know why this error came out. Because of this error i can't integrate my data.... I think one of the function i use trigger as.sparse issue but still i don't know how to handle this problem please help me

scrna-seq
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written by kayah • kayah

Please do not post screenshots for text data. Use copy and paste and then format the data with code option (101010 button in edit mode).

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written by GenoMax GenoMax

thank you for your kind advice!

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written by kayah • kayah

Step1 would be to remove all pipes and find out which function chokes.

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written by ATpoint ATpoint

Which code is the Step 1 process...??

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written by kayah • kayah

I rephrase: Execute every line of code step by step without pipes and report at which step the error comes up.

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written by ATpoint ATpoint 
library(devtools)
library(dplyr)
library(ggplot2)
library(Seurat)
library(SeuratObject)
library(sp)
library(patchwork)
library(harmony)
library(Rcpp)
?library(SeuratWrappers)
library(clustree)
library(cowplot)
library(RColorBrewer)
library(pheatmap)
install.packages("FindvariableFeatures")

young_1 <- readRDS('~/Desktop/GSE137869/2ndtry/seurat_object_young1.rds')
young_2 <- readRDS('~/Desktop/GSE137869/2ndtry/seurat_object_young2.rds')
old_1 <- readRDS('~/Desktop/GSE137869/2ndtry/seurat_object_old1.rds')
old_2 <- readRDS('~/Desktop/GSE137869/2ndtry/seurat_object_old2.rds')

young_1 <- NormalizeData(young_1)
young_2 <- NormalizeData(young_2)
old_1 <- NormalizeData(old_1)
old_2 <- NormalizeData(old_2)

library(glmGamPoi)

WAT <- merge(young_1, y = c(young_2, old_1, old_2), 
             add.cell.ids = c("young1", "young2", "old1", "old2"),
             project = "WAT")
WAT <- NormalizeData(WAT) 
WAT <- FindVariableFeatures(WAT,selection.method = "vst", nfeatures = 2000)
all.genes <- rownames(WAT)
WAT <-ScaleData(WAT, features = all.genes)
View(WAT@meta.data)
WAT <- SCTransform(WAT, vars.to.regress = c("percent.mt"))

SCTransform spot is where error happens... I want to transform data to SCTform please help me!!

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written by kayah • kayah

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