Expression of gene of interest across conditions in single-cell data

1

Hi everyone,

I have a tpm gene expression matrix (single-cell RNA-seq data) from a publication which I would like to use to explore expression of my gene of interest. The single-cell data consists of cells from 10 conditions. I'd like to look at expression of my gene of interest in these conditions. Ultimately I'd like to create a visualisation showing the proportion of cells in each condition that express my gene of interest.

I've created a SingleCellExperiment object from the tpm counts, but I'm not sure how to determine the proportion of cells in each condition that express my gene of interest, what cutoff to use for expression, etc. Additionally, as well as proportion of cells, is there a good way to determine average expression of the gene for each condition? Something simple like a bar plot is all I wish to produce. Any recommended packages etc? Any advice is greatly appreciated!

Thank you!

Edit to add example data:

# SCE object 

class: SingleCellExperiment 
dim: 31211 2098 
metadata(0):
assays(1): tpm
rownames(31211): ENSMUSG00000000001 ENSMUSG00000000003 ... ENSMUSG00000118639
ENSMUSG00000118640
rowData names(2): V1 V2
colnames(2098): SRR5993298 SRR5993299 ... SRR5995502 SRR5995505
colData names(2): V1 sample_type
reducedDimNames(0):
spikeNames(0):

# sample_type stored in colData is condition for each cell/run (SRRxxxx) in same order as colnames 

sample_type
<fctr>
659 CK_2w_m2            
663 CK_2w_m2            
664 CK_2w_m2            
665 CK_2w_m2            
666 CK_2w_m2            
667 CK_2w_m2


singlecell


scater


tpm


seurat


Rna-seq

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2 hours ago by


kz

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