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combineCellProximityGenes.rst

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combineCellProximityGenes

combineCellProximityGenes

Description

Combine ICG scores in a pairwise manner.

Usage

combineCellProximityGenes(...)

Arguments

Argument Description
... Arguments passed on to combineInteractionChangedGenes#combineinteractionchangedgenes list("n", " ", list(list(list("cpgObject")), list("ICG (interaction changed gene) score object")), "n", " ", list(list(list("selected_ints")), list("subset of selected cell-cell interactions (optional)")), "n", " ", list(list(list("selected_genes")), list("subset of selected genes (optional)")), "n", " ", list(list(list("specific_genes_1")), list("specific geneset combo (need to position match specific_genes_2)")), "n", " ", list(list(list("specific_genes_2")), list("specific geneset combo (need to position match specific_genes_1)")), 
"\n", "    ", list(list(list("min_cells")), list("minimum number of target cell type")), "\n", "    ", list(list(list("min_int_cells")), list("minimum number of interacting cell type")), "\n", "    ", list(list(list("min_fdr")), list("minimum adjusted p-value")), "\n", "    ", list(list(list("min_spat_diff")), list("minimum absolute spatial expression difference")), "\n", "    ", list(list(list("min_log2_fc")), list("minimum absolute log2 fold-change")), "\n", "    ", list(list(list("do_parallel")), 
    list("run calculations in parallel with mclapply")), "\n", "    ", list(list(list("cores")), list("number of cores to use if do_parallel = TRUE")), "\n", "    ", list(list(list("verbose")), list("verbose")), "\n", "  ")

Seealso

combineInteractionChangedGenes#combineinteractionchangedgenes