Are Variable Features ranked in seurat?
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2.4 years ago
am ▴ 40

Dear all,

does anybody know if variable features obtained by FindVariableFeatures(object, selection.method = "vst", nfeatures = 2000) in Seurat are ranked?

If I look at the top variable genes in var_gene

var_genes <- object[["integrated"]]@var.features

I see e.g. : "Ccl19" "Cxcl13" "Cxcl2" "Mt1" "Ube2c" "Ccl7" etc.

These genes are not alphabetically ordered.

Then if I do:

head(x = HVFInfo(object ))

I see:

             mean   variance variance.standardized
Ccl19   4.160807364 1.24052609            1.90000219
Cxcl13  1.441161138 1.90205720            2.14033622
Cxcl2   0.334520728 0.86124531            2.24994302
Mt1     0.868732859 1.35599061            1.78447681
Ube2c  -0.003635472 0.06066679            0.06802445
Ccl7    1.484888892 1.96883363            3.03841544

The genes are reported in the same order as in var_genes but if I look at the variance or the variance.standardized they do not seem to be sorted.

So my question is, if I want to get the top 5 genes among the most variable ones how should I do?

I hope I was clear, thank you all in advance!

seurat FindVariableFeatures rank • 954 views
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