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subset function in v3 #1053

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nasqar opened this issue Jan 14, 2019 · 3 comments
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subset function in v3 #1053

nasqar opened this issue Jan 14, 2019 · 3 comments

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@nasqar
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nasqar commented Jan 14, 2019

Hi,
Background: We developed an RShiny web interface SeuratWizard for seurat v2 (guided clustering workflow) and I am currently trying to migrate it to v3.

For the subset function, is there a way to use a variable containing the subset name. For example:
var1 = "name"
subset(x = object, subset = var1 > low & var1 < high)

Could be a simple oversight on my part. Appreciate the help
@mojaveazure
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Much like R's subset function, subset.Seurat is designed for interactive use only. While we currently don't offer a programmatic way to subset Seurat objects based on feature expression, this can be accomplished relatively easily using which and FetchData

expr <- FetchData(object = object, vars = var1)
object[, which(x = expr > low & expr < high)]

@nasqar
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nasqar commented Jan 16, 2019

Yes this works well. Thanks for the explanation.

@nasqar nasqar closed this as completed Jan 16, 2019
This was referenced May 17, 2019
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@nicodemus88 nicodemus88 mentioned this issue May 31, 2019
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esrice added a commit to WarrenLab/single-cell that referenced this issue Feb 25, 2020
@esrice
can't use subset() programatically
3f7b213 
see satijalab/seurat#1053
@timoast timoast mentioned this issue Mar 16, 2020
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@mojaveazure mojaveazure mentioned this issue Apr 13, 2020
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@mojaveazure mojaveazure mentioned this issue Feb 12, 2021
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@jindall
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jindall commented Jul 5, 2022

@mojaveazure
how to make a subset of seurat object that contains the cells expressing just the genes in the gene_list:
gene_list hs 4000 genes in total
text_case

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@jindall @mojaveazure @nasqar