Question: Cluster using known marker genes (Seurat)
0
gravatar for V
8 months ago by
V230
UK/London
V230 wrote:

Hello,

Using the seurat pipeline (v3) is there a way to cluster using known marker genes, or a set of genes that you pass into the package as opposed to the variable genes which are the ones used in the vignette? If so how? If anyone could provide a coded example that would be amazing.

Thank you!!

ADD COMMENTlink modified 8 months ago by Arup Ghosh2.7k • written 8 months ago by V230
1
gravatar for Arup Ghosh
8 months ago by
Arup Ghosh2.7k
India
Arup Ghosh2.7k wrote:

While running the RunPCA function instead of VariableFeatures(object = obj) provide a list of marker genes you are interested in.

Code example:

pbmc <- RunPCA(pbmc, features = c('LYZ','CCL3','CCL5','CCL4','IL8','HLA-DRB1'))
ADD COMMENTlink modified 8 months ago • written 8 months ago by Arup Ghosh2.7k

Thank you. Sorry naive question coming up.

If this was a long gene list compiled with 1000+ genes, would the appropriate way to pass it in be a csv file? So something like:

e.g

genes <- genelist.csv

MySeurat <- RunPCA(MySeurat, features  = genes))
ADD REPLYlink modified 8 months ago • written 8 months ago by V230

You have modify the first line of the code.

genes <- read.csv('genelist.csv')[,1]
ADD REPLYlink written 8 months ago by Arup Ghosh2.7k
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