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!