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!
• 283 views
•
link
0 answers
No answers yet.
Log in to answer this question.
Use the
meta.dataparameter ofCreateSeuratObject()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.I think I got it now, thanks!
You must have the GEM well barcode id and associated cell origin to create such subsets. The barcodes are present in
orig.identcolumn.