Calculate spots' gene set score from the in-house or user-defined gene sets.
Arguments
- SpaCET_obj
An SpaCET object.
- GeneSets
A string for in-house gene sets, or a list object for user-defined gene sets. See details.
Details
1) Set `GeneSets` as "Hallmark", "CancerCellState", or "TLS" to use the in-house gene sets. "Hallmark": https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#H
"CancerCellState": https://www.nature.com/articles/s41588-022-01141-9
"TLS": https://www.researchsquare.com/article/rs-3921508
2) Set `GeneSets` as a list to use the user-defined gene sets. Each entry should be a vector of gene symbols.
The function `ScoreSignatures_UCell` from `UCell` is used to calculate gene-set scores. https://bioconductor.org/packages/release/bioc/html/UCell.html.