combineCellProximityGenes: combineCellProximityGenes

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Combine CPG scores in a pairwise manner.

Usage

combineCellProximityGenes(
  cpgObject,
  selected_ints = NULL,
  selected_genes = NULL,
  specific_genes_1 = NULL,
  specific_genes_2 = NULL,
  min_cells = 5,
  min_int_cells = 3,
  min_fdr = 0.05,
  min_spat_diff = 0,
  min_log2_fc = 0.5,
  do_parallel = TRUE,
  cores = NA,
  verbose = T
)

Arguments

cpgObject	cell proximity gene score object
selected_ints	subset of selected cell-cell interactions (optional)
selected_genes	subset of selected genes (optional)
specific_genes_1	specific geneset combo (need to position match specific_genes_2)
specific_genes_2	specific geneset combo (need to position match specific_genes_1)
min_cells	minimum number of target cell type
min_int_cells	minimum number of interacting cell type
min_fdr	minimum adjusted p-value
min_spat_diff	minimum absolute spatial expression difference
min_log2_fc	minimum absolute log2 fold-change
do_parallel	run calculations in parallel with mclapply
cores	number of cores to use if do_parallel = TRUE
verbose	verbose

Value

cpgObject that contains the filtered differential gene scores

Examples

    combineCellProximityGenes(gobject)

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