Integrate query cell types with reference cell types

This function normalizes query data to reference data using PCA-space quantile normalization, performed separately for each cell type.

IntegrateData(ref_path, query_path, Celltype_col)

Arguments

ref_path

Path to reference CSV file.

query_path

Path to predicted query CSV file.

Celltype_col

Character. Column containing cell-type labels.

Value

A data.frame containing normalized query marker values.

Details

Normalization is performed separately per cell type. Only numeric marker columns are processed.

Examples

if (FALSE) { # \dontrun{
corrected <- IntegrateData(
  ref_path = "Reference_Data/CyTOF_train.csv",
  query_path = "Query_Data/CITEseq_test.csv",
  Celltype_col = "cluster.orig"
)
} # }