SpaCET.GeneSetScore: Calculate gene set score for each spot.

In data2intelligence/SpaCE: Spatial Cellular Estimator for Tumors

Calculate gene set score for each spot.

Description

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.

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.

Value

An SpaCET object

Examples

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

data2intelligence/SpaCE documentation built on Nov. 15, 2024, 12:03 a.m.