calculateMetaTable

calculates the average gene expression for one or more (combined) annotation columns.

calculateMetaTable(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  metadata_cols = NULL,
  selected_genes = NULL
)

Arguments

gobject

giotto object

expression_values

expression values to use

metadata_cols

annotation columns found in pDataDT(gobject)

selected_genes

subset of genes to use

Value

data.table with average expression values for each gene per (combined) annotation

Examples

data(mini_giotto_single_cell)
#> Warning: data set ‘mini_giotto_single_cell’ not found

# show cell metadata
pDataDT(mini_giotto_single_cell)
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Error: object 'mini_giotto_single_cell' not found

# show average gene expression per annotated cell type
calculateMetaTable(mini_giotto_single_cell,
                   metadata_cols = 'cell_types')
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Error: object 'mini_giotto_single_cell' not found