Adjust Expression Values

adjustGiottoMatrix()

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

A 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)