SC (single cell) + CP (clusterProfiler) => SCCP => SC2P (single cell to pathway)
- score cell states by pathways (e.g., GSVA)
- identify cell type significant pathways
> eres <- scKEGG.Seurat(pbmc)
'select()' returned 1:1 mapping between keys and columns
Estimating GSVA scores for 356 gene sets.
Estimating ECDFs with Gaussian kernels
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> head(eres, 3)
ID logFC AveExpr t P.Value adj.P.Val B
1 hsa00290 0.5263822 0.5108176 181.02353 0.000000e+00 0.000000e+00 3412.9098
2 hsa00290 0.5656179 0.5108176 26.81641 2.885105e-140 1.027097e-137 309.6167
3 hsa00290 0.5369375 0.5108176 130.95099 0.000000e+00 0.000000e+00 2646.4178
ident Description
1 Naive CD4 T Valine, leucine and isoleucine biosynthesis
2 Platelet Valine, leucine and isoleucine biosynthesis
3 B Valine, leucine and isoleucine biosynthesis