adjustGiottoMatrix: adjustGiottoMatrix

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

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

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 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)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.