Adjust expression values#

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Last Updated: Mar 11, 2023

Description#

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

Usage#

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

Arguments#

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

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 function to remove known batch effects and to adjust expression values according to provided covariates.

Value#

giotto object or exprObj