Question about scRNA-seq cell annotation using SingleR

Question

[Yingying]

Hi guys,

This is my first time analyzing a scRNA-seq dataset, and now I'm a bit stuck at the cell annotation step with SingleR. My dataset is from an enriched population from PBMC, and I'm mostly interested in different types of blood cells. However, within the Human Primary Cell Atlas data from celldex() package, there are also cell types besides blood cells, such as muscle cells. Does anyone have an idea of how to remove certain cell types from the reference dataset?

Any response would be appreciated!

Thanks

Answer 1

[ATpoint]

The function returns a SummarizedExperiment object that following base R subsetting rules. An example:

library(celldex)

hpca <- HumanPrimaryCellAtlasData()

# List available labels via the colData() -- several levels of labels available, like label.main, label.fine etc...
colData(hpca)

# Subset the SummarizedExperiment following base R rules for three celltypes using label.main
wanted <- c("Monocyte", "GMP", "B_cell")
hpca_subset <- hpca[,hpca$label.main %in% wanted]

[Yingying]

Hi, Thanks so much for your help!!