Cluster using known marker genes (Seurat)

Question

[V]

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!!

Answer 1

[Arup Ghosh]

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'))

[V]

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))

[Arup Ghosh]

You have modify the first line of the code.

genes <- read.csv('genelist.csv')[,1]