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GabrielHoffman/get_raw_counts.R

Created February 1, 2024 15:31
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Get raw counts using zellkonverter
Raw
get_raw_counts.R
library(zellkonverter)
library(SingleCellExperiment)
file = "240118_PsychAD_FULL_1494_subclass_EN_NF_hvg3k_umap.h5ad"
sce = readH5AD(file, use_hdf5=TRUE, verbose=TRUE, raw=TRUE)
# normalized counts
assay(sce, "X")[1:3, 1:3]
# see "alternative expression", i.e. raw counts
altExpNames(sce)
# Put raw counts into main
sce2 = swapAltExp(sce, "raw")
# raw counts
assay(a, "X")[1:3, 1:3]
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