How to create seurat object from a loom file directly??

[shaaaarpy]

I have a loom file and want to perform differential expression analysis. How should i proceed?

[mschilli87]

@shaaaarpy: see https://satijalab.org/loomR/loomR_tutorial.html#loomr-and-seurat

[shaaaarpy]

This tutorial does not show how to create seurat object from loom object. Can you please elaborate on this?

[mschilli87]

The tutorial links to this vignette showing how to tun Seurat on loom files. There is no need to create a Seurat object as loom files operate by memory-mapping data on disk while a Seurat object would be loading all data to RAM.

[Sophia409]

@shaaaarpy I have the same question as you. I also need to convert loom file to seurat object. Do you find any solutions?

[danaschwalbe]

To convert a loom file to a seurat object, you must first load the loom file using the connect() function in the loomR package, and then convert it to a seurat object using the as.Seruat() function in the Seurat package.

Example: loomasseurat<-as.Seurat(myloomfile,cells="CellIDs",features="Gene")