adjustGiottoMatrix — adjustGiottoMatrix • Giotto

Adjust expression values to account for known batch effects or technological covariates.

adjustGiottoMatrix(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  batch_columns = NULL,
  covariate_columns = NULL,
  return_gobject = TRUE,
  update_slot = c("custom")
)

Arguments

gobject: giotto object
expression_values: expression values to use
batch_columns: metadata columns that represent different batch (max = 2)
covariate_columns: metadata columns that represent covariates to regress out
return_gobject: boolean: return giotto object (default = TRUE)
update_slot: expression slot that will be updated (default = custom)

Value

giotto object

Details

This function implements the removeBatchEffect function to remove known batch effects and to adjust expression values according to provided covariates.

Examples


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

adjust_gobject = adjustGiottoMatrix(mini_giotto_single_cell)
#> Error in adjustGiottoMatrix(mini_giotto_single_cell): Metadata for either different batches or covariates must be
#>             provided.