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rezakj / iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
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How to normalize data with single condition? #29

Open bioysu opened 3 years ago

bioysu commented 3 years ago

Hello,

I created an object with data of single condition and tried to normalized it with ranked.glsf. But main.data is empty. I also tried to normalized it with no.norm. But main.data is still empty. Count you tell me how to fix it?

my.obj <- norm.data(my.obj, norm.method = "ranked.glsf", top.rank = 500) my.obj <- norm.data(my.obj, norm.method = "no.norm")

rezakj commented 3 years ago

2 ways to do this; if you don't want to filter cells:

my.obj@main.data <- my.obj@raw.data

And if you want to filter cells:

my.obj <- cell.filter(my.obj,
    min.mito = 0,
    max.mito = 0.05,
    min.genes = 200,
    max.genes = 2400,
    min.umis = 0,
    max.umis = Inf)

And if you don't want to normalize skip the normalization step.

Hope this helps!