Seurat V3 Workflow about swne HOT 13 CLOSED

Ah sorry it should be GetAssayData instead of AssayData. Let me know if that works!

from swne.

It still did not work :/

`

AssayData(se.obj, slot = "counts") <- FilterData(GetAssayData(se.obj, slot = "counts"), min.samples.frac = 0.0025, min.nonzero.features = 200, trim = 0.0025)

#Error in AssayData(se.obj, slot = "counts") <- FilterData(GetAssayData(se.obj, :
could not find function "AssayData<-"

GetAssayData(se.obj, slot = "counts") <- FilterData(GetAssayData(se.obj, slot = "counts"), min.samples.frac = 0.0025, min.nonzero.features = 200, trim = 0.0025)

#Error in GetAssayData(se.obj, slot = "counts") <- FilterData(GetAssayData(se.obj, :
could not find function "GetAssayData<-"`

from swne.

Are you sure you have Seurat V3 installed? Also it should be:

SetAssayData(se.obj, slot = "counts") <- FilterData(GetAssayData(se.obj, slot = "counts"), min.samples.frac = 0.0025, min.nonzero.features = 200, trim = 0.0025)

from swne.

> SetAssayData(se.obj, slot = "counts") <- FilterData(GetAssayData(se.obj, slot = "counts"), min.samples.frac = 0.0025, min.nonzero.features = 200, trim = 0.0025)

#Error in SetAssayData(se.obj, slot = "counts") <- FilterData(GetAssayData(se.obj,  : 
  could not find function "SetAssayData<-"

> packageVersion("Seurat")
[1] ‘3.0.2’

I do not think you can use the AssayData() commands in the way you have described above.

from swne.

I have also tried running through the Gene Expression Quickstart with Seurat, but run into an error where the "RunSWNE" does not seem to be compatible with a seurat v3 object.

## Load object
load("/path/Ma_Vasc_6_res0.75.Robj")
obj <- Ma_Vasc_6_res0.75

## Extract clusters
clusters <- obj$seurat_clusters

## Select genes to embed
genes.embed <- c("Aplnr", "Apln", "Cryab", "Gata5", "Pi16")

## Run SWNE
swne.embedding <- RunSWNE(obj, k = 16, genes.embed = genes.embed)

Error in UseMethod("RunSWNE") : 
  no applicable method for 'RunSWNE' applied to an object of class "Seurat"

packageVersion("Seurat")
# ‘3.0.2’
packageVersion("swne")
# ‘0.2.21’

from swne.

Ahh sorry you're right. For the filtering it should be something more like:

counts <- FilterData(GetAssayData(se.obj, slot = "counts"), min.samples.frac = 0.0025, min.nonzero.features = 200, trim = 0.0025)
se.obj <- SetAssayData(se.obj, slot = "counts", new.data = counts)

from swne.

Oh so the latest version of swne should be 0.5.6. Can you try reinstalling it and see if RunSWNE works then?

from swne.

Certainly, is swne 0.5.6 only available for R version 3.6.1? I just tried installing on R 3.5.1 and R 3.5.3 and neither worked.

Thanks!

from swne.

Ah sorry yeah I built it on R3.6 so I think >= R3.6.1 is necessary for installation

from swne.

I updated to R version 3.6.1 (2019-07-05) -- "Action of the Toes" but am unfortunately still encountering the same error :/

install.packages("swne")
Warning in install.packages :
  package ‘swne’ is not available (for R version 3.6.1)

This does not appear to be a problem with other packages (Seurat, ggplot2)

from swne.

swne is not on CRAN so you can't use install.packages. You can install it with devtools using the instructions on this github page

from swne.

Ahh, that fixed the issue - my mistake for not seeing that earlier. I was able to work through swne with a seurat v3 object.

Thanks!

from swne.

Great! Let me know if you have any other issues!

from swne.