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Cluster using known marker genes (Seurat)

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!!

seurat single cell rnaseq rstudio rnaset
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updated by Arup Ghosh Arup Ghosh • written by V V

1 answer

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'))
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written by Arup Ghosh Arup Ghosh

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))
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written by V V

You have modify the first line of the code.

genes <- read.csv('genelist.csv')[,1]
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written by Arup Ghosh Arup Ghosh

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