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Calculate spots' gene set score from the in-house or user-defined gene sets.

Usage

SpaCET.GeneSetScore(SpaCET_obj, GeneSets)

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.

Value

An SpaCET object

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.

Examples

SpaCET_obj <- SpaCET.GeneSetScore(SpaCET_obj, GeneSets="Hallmark")