createSpatialEnrich: createSpatialEnrich

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

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 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 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 return_gobject return giotto object

See Also

runSpatialEnrich

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.