Adjust expression values#
Last Updated: Oct 02, 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#
|
giotto object |
|
spatial unit |
|
feature type |
|
expression values to use |
|
metadata columns that represent different batch (max = 2) |
|
metadata columns that represent covariates to regress out |
|
boolean: return giotto object (default = TRUE) |
|
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