createSpatialEnrich: createSpatialEnrich

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

createSpatialEnrich

Description

Function to calculate gene signature enrichment scores per spatial position using an enrichment test.

Usage

createSpatialEnrich(...)

Arguments

...

Arguments passed on to runSpatialEnrich gobject Giotto object enrich_method method for gene signature enrichment calculation sign_matrix Matrix of signature genes for each cell type / process expression_values expression values to use reverse_log_scale reverse expression values from log scale min_overlap_genes minimum number of overlapping genes in sign_matrix required to calculate enrichment (PAGE) logbase log base to use if reverse_log_scale = TRUE p_value calculate p-value (default = FALSE) n_times (page/rank) number of permutation iterations to calculate p-value rbp_p (rank) fractional binarization threshold (default = 0.99) num_agg (rank) number of top genes to aggregate (default = 100) max_block number of lines to process together (default = 20e6) top_percentage (hyper) percentage of cells that will be considered to have gene expression with matrix binarization output_enrichment how to return enrichment output name to give to spatial enrichment results, default = PAGE verbose be verbose return_gobject return giotto object

See Also

runSpatialEnrich

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.