Seurat: Where does Seurat store variable gene information?

[GHAStVHenry]

Ran RunCCA/AlignSubspace, then when execute FindVariableGenes, @genes.hvg results in Error: no slot of name "genes.hvg" for this object of class "seurat"

[mojaveazure]

Hi Gervaise, the Seurat object doesn't have a slot called genes.hvg; as seen in the docs, FindVariableGenes stores the variable genes in the var.genes slot, with the means and dispersion values stored in the hvg.info slot.

[GHAStVHenry]

I'm sorry, I named it incorrectly, I meant var.genes.

When I just do FindVariableGenes, it populates @var.genes.

If I do FindVariableGenes after RunCCA/AlignSubspace, FindVariableGenes does NOT populate @var.genes. If I want to get the var.genes, I have to filter the @hvg.info myself.

[mojaveazure]

I can't replicate that:

> data("pbmc_small")
> pbmc1 <- SubsetData(object = pbmc_small, cells.use = [email protected][1:40])
> pbmc2 <- SubsetData(object = pbmc_small, cells.use = [email protected][41:80])
> [email protected]$group <- "group1"
> [email protected]$group <- "group2"
> pbmc_cca <- RunCCA(object = pbmc1, object2 = pbmc2)
Running CCA
Merging objects
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Scaling data matrix
  |=============================================================| 100%
> pbmc_cca <- AlignSubspace(object = pbmc_cca, reduction.type = "cca", grouping.var = "group", dims.align = 1:2)
Rescaling group 1
Scaling data matrix
  |=============================================================| 100%
Rescaling group 2
Scaling data matrix
  |=============================================================| 100%
Aligning dimension 1
   |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed = 00s
   |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed = 00s
Aligning dimension 2
   |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed = 00s
   |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed = 00s
> [email protected]
 [1] "LTB"       "EAF2"      "PIK3IP1"   "KHDRBS1"   "SRSF7"    
 [6] "S1PR4"     "LYAR"      "SATB1"     "IL17RA"    "POP7"     
[11] "ZNF330"    "COPS6"     "PPBP"      "HIST1H2AC" "TALDO1"   
[16] "ACRBP"     "VDAC3"     "GNLY"      "PTGDR"     "ARHGDIA"  
[21] "PCMT1" 
> pbmc_cca <- FindVariableGenes(object = pbmc_cca, do.plot = FALSE)
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> [email protected]
 [1] "LTB"       "EAF2"      "CD19"      "KIAA0125"  "CYB561A3" 
 [6] "IGLL5"     "PIK3IP1"   "KHDRBS1"   "CCR7"      "ACSM3"    
[11] "SRSF7"     "S1PR4"     "LYAR"      "SATB1"     "IL17RA"   
[16] "POP7"      "ZNF330"    "COPS6"     "PPBP"      "PF4"      
[21] "HIST1H2AC" "TALDO1"    "CA2"       "ACRBP"     "TSC22D1"  
[26] "VDAC3"     "GNLY"      "PTGDR"     "ARHGDIA"   "PCMT1"    
[31] "S100B" 

The var.genes slot is different, and therefore populated by FindVariableGenes after running RunCCA/AlignSubspace.

[GHAStVHenry]

Donno what to tell you, it's not populating for me. It's OK, I just pulled the genes by slicing the @hvg.info with my cutoffs.

Thanks,
Gervaise

[brianpenghe]

Ran RunCCA/AlignSubspace, then when execute FindVariableGenes, @genes.hvg results in Error: no slot of name "genes.hvg" for this object of class "seurat"

In Seurat3 it's stored at
Object@assays[email protected]