DataPreProcess

Preprocess expression data for pathway analysis.

Usage

DataPreProcess(
  x,
  pathwaydata,
  Seurat.object = FALSE,
  assay = "RNA",
  slot = "data",
  scale.data = TRUE
)

Arguments

x

A Seurat object OR a gene-by-cell normalized expression matrix

pathwaydata

Pathway data from the output of LoadPathway()

Seurat.object

Logical; whether x is a Seurat object

assay

Assay to use if x is a Seurat object (default = "RNA")

slot

Slot to extract from Seurat object (default = "data")

scale.data

Logical; whether to apply row-wise z-score scaling (default = TRUE). If FALSE, the filtered expression matrix is returned as-is without any scaling.

Value

A gene-by-cell expression matrix of pathway genes. If scale.data = TRUE (default), values are row-wise z-scored; if scale.data = FALSE, raw input filtered values are returned.

Examples

if (FALSE) { # \dontrun{
DataPreProcess(seurat_obj, pathwaydata, Seurat.object = TRUE)
DataPreProcess(norm_matrix, pathwaydata)
DataPreProcess(norm_matrix, pathwaydata, scale.data = FALSE)
} # }