I was using Seurat to analysis single-cell RNA Seq. And I was interested in only one cluster by using the Seurat. Does anyone know how to achieve the cluster's data(.csv file) by using Seurat or any other method that can do this function? Thank you!
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1$\begingroup$ A cluster may contain different types of data. Do you want the specific cells, expression for each cell, average expression, cluster markers, etc.? $\endgroup$– burgerCommented Feb 18, 2019 at 23:13
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$\begingroup$ Yes even a cluster contain different types of data. I still want to obtain that cluster's data including its each cell and gene expression for further analysis. $\endgroup$– huaCommented Feb 19, 2019 at 3:23
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1$\begingroup$ I think that the Seurat tutorials had some information about this. Did you read them? Have you tried something? $\endgroup$– llrsCommented Feb 19, 2019 at 10:12
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1 Answer
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You can access data within the Seurat object using GetAssayData, and extract a list of cell names for the cluster you're interested in using WhichCells:
library(Seurat)
cells.use <- WhichCells(object = pbmc_small, ident = 1)
expr <- GetAssayData(object = pbmc_small, assay.type = "RNA", slot = "data")[, cells.use]
expr <- as(Class = 'matrix', object = expr)
write.csv(x = expr, file = "expression_cluster1.csv", quote = FALSE)
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$\begingroup$ Hi TimStuart, thank you for your advice, and it works well in the RStudio. But when I use this script in cypress it shows the error "Error in as(Class = "matrix", object = expr), could not find function "as" Execution halted". Do you know how to solve this problem? $\endgroup$– huaCommented Feb 22, 2019 at 5:35
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$\begingroup$ I don't know what cypress is, but if you're running it in a script you'll need to load the methods and utils libraries $\endgroup$ Commented Feb 22, 2019 at 14:11
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$\begingroup$ Hi TimStuart, thank you for your reply, and if it is possible could you please tell my what kind of the utils libraries that I should load? $\endgroup$– huaCommented Feb 22, 2019 at 16:25
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library(methods); library(utils)$\endgroup$ Commented Feb 22, 2019 at 17:24 -
$\begingroup$ Hi TimStuart, nowadays thank you for the Seurat's update, we can analysis several samples together. And I would like to know whether we can obtain the specific sample's specific cluster gene expression profile by using the same code "cells.use <- WhichCells(object = pbmc_small, ident = 1) expr <- GetAssayData(object = pbmc_small, assay.type = "RNA", slot = "data")[, cells.use] expr <- as(Class = 'matrix', object = expr) write.csv(x = expr, file = "expression_cluster1.csv", quote = FALSE)"? $\endgroup$– huaCommented Oct 2, 2019 at 22:16