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Subsetting dataset to create 2 seurat objects

I'm aligning two groups (old vs young) using this tutorial

The tutorial has the two groups in separate files (control & stim):

ctrl.data <- read.table(file = "../data/immune_control_expression_matrix.txt.gz", sep = "\t")
stim.data <- read.table(file = "../data/immune_stimulated_expression_matrix.txt.gz", sep = "\t")

then set up control object

ctrl <- CreateSeuratObject(counts = ctrl.data, project = "IMMUNE_CTRL", min.cells = 5)
stim <- CreateSeuratObject(counts = stim.data, project = "IMMUNE_STIM", min.cells = 5)

I have a matrix of gene counts (rows) and 3 cell types (columns) gathered from young and old mice.

How can I separate my dataset to create separate Seurat objects for young and old? An example column name is young_MPP_179.

Thanks!

r seurat rna-seq
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written by planetearth • planetearth

Use the meta.data parameter of CreateSeuratObject() to supply a data.frame with the corresponding information: each row in that data.frame should correspond to a cell name (= colname) of the matrices you read in; you can then use the columns to specify which cell belongs to either OLD or YOUNG.

You will then be able to use the SubsetData() function.

• 0 views • link
written by Friederike Friederike

You must have the GEM well barcode id and associated cell origin to create such subsets. The barcodes are present in orig.ident column.

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written by Arup Ghosh Arup Ghosh

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