adjustGiottoMatrix: Adjust expression values
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

adjustGiottoMatrix

R Documentation

Adjust expression values

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 (e.g. "cell")
`feat_type`	feature type (e.g. "rna", "dna", "protein")
`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.