`adjustGiottoMatrix`¶

adjustGiottoMatrix

Description¶

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

Usage¶

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

Arguments¶

Argument	Description
`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)

Details¶

This function implements the ``removeBatchEffect` <#removebatcheffect>`_ function to: remove known batch effects and to adjust expression values according to provided covariates.

Value¶

giotto object

Examples¶

data(mini_giotto_single_cell)

adjust_gobject = adjustGiottoMatrix(mini_giotto_single_cell)