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subsetting loom file #80

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menage95 opened this issue Oct 20, 2023 · 0 comments
Open

subsetting loom file #80

menage95 opened this issue Oct 20, 2023 · 0 comments

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@menage95
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Hello,

I have connected to a loom file and would like to extract the matrix counts with gene names for 2 different column attributes. I can do it with one column attribute but ideally need both plus gene names. Below is what I have so far:

lfile <- connect(filename = "file.loom", mode = "r+", skip.validate = TRUE)
data<- lfile[["matrix"]][lfile$col.attrs$Tissue[] == "Midbrain",  ] 

Any help would be much appreciated as all the above returns is a large data frame with no cell numbers or gene names.

Thanks

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