Get the batch-corrected integrated gene expresssions

Get the batch-corrected integrated gene expresssions

getIntegratedData(
  SRTProj,
  species = "Human",
  Method = c("iSC.MEB", "PRECAST"),
  custom_housekeep = NULL,
  only.var.features = TRUE,
  add_empty_counts = FALSE
)

Arguments

SRTProj

a SRTProject object after finishing integration analysis using Integrate_PRECAST or Integrate_iSCMEB.

species

a string, one of "Human", "Mouse" and "Unknown", default as "Human".

Method

a string, one of "iSC.MEB" and "PRECAST", specify which method is used to remove the batch effects in the gene expression levels.

custom_housekeep

a string vector, a group of user-specified housekeeping genes used for removing batch.

only.var.features

a logical value, whether only return the variable genes.

add_empty_counts

a logical value, whether add a empty count matrix. This argument makes it easy to transfer the returned SpatialExperiment object to a Seurat object using as.Seurat.

Value

return a SpatialExperiment object with integrated normalized gene expression matrix and other information from the SRTProject object.