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)

adjust_gobject = adjustGiottoMatrix(mini_giotto_single_cell)