error in "SelectIntegrationFeatures" function #9217
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morikazu1209
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Hello.
I would like to thank the team for this wonderful tool.
I am posting this discussion for help.
I am integrating two seuratobjects and then splitting the integrating data by split.by "GROUP" to compare the two seuratobjects.
However, after I enter "features <- SelectIntegrationFeatures(object.list = Groupbignormalized.list)", which you can find at the bottom of the entire codes below, I receive the error "Error in as.list.default(X) : no method for coercing this S4 class to a vector" and I cannot find its solution. Thank you for your kind support in advance.
Group1.data <- Read10X(data.dir = "./data/Group1/filtered_gene_bc_matrices/Control/")
Group1 <- CreateSeuratObject(counts = Group1.data, project = "GROUP1", min.cells = 3, min.features = 200)
[email protected]$GROUP <- "control"
head([email protected]$control)
Group1
Group2.data <- Read10X(data.dir = "./data/Group2/filtered_gene_bc_matrices/Sparsentan/")
Group2 <- CreateSeuratObject(counts = Group2.data, project = "GROUP2", min.cells = 3, min.features = 200)
[email protected]$GROUP <- "drug"
Group2
Group1 [["percent.mt"]] <- PercentageFeatureSet(Group1, pattern = "^mt-")
VlnPlot(Group1, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
Group2 [["percent.mt"]] <- PercentageFeatureSet(Group2, pattern = "^mt-")
VlnPlot(Group2, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
Group1 <- subset(Group1, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 10)
Group2 <- subset(Group2, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 10)
Group1 <- NormalizeData(Group1, normalization.method = "LogNormalize", scale.factor = 10000)
Group1 <- NormalizeData(Group1)
Group1
Group2 <- NormalizeData(Group2, normalization.method = "LogNormalize", scale.factor = 10000)
Group2 <- NormalizeData(Group2)
Group2
Groupbig.normalized <- merge(
Group1,
y = Group2,
add.cell.ids = c("control", "drug"),
project = "GROUPBIG",
merge.data = TRUE)
Groupbig.normalized
Groupbignormalized.list <- SplitObject(Groupbig.normalized, split.by = "GROUP")
Groupbignormalized.list <- FindVariableFeatures(Groupbig.normalized, selection.method = "vst", nfeatures = 2000)
features <- SelectIntegrationFeatures(object.list = Groupbignormalized.list)
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