run_proportion_raw: Generate cell type proportion raw

In SydneyBioX/scFeatures: scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

Generate cell type proportion raw

Description

This function calculates the proportions of cells belonging to each cell type. The input data must contain sample and celltype metadata column. The function supports scRNA-seq and spatial proteomics. The function returns a dataframe with samples as rows and cell types as columns.

Usage

run_proportion_raw(data, type = "scrna", ncores = 1)

Arguments

data	A list object containing data matrix and celltype and sample vector.
type	The type of dataset, either "scrna", "spatial_t", or "spatial_p".
ncores	Number of cores for parallel processing.

Value

a dataframe of samples x features. The features are in the form of celltype a, celltype b, with the number representing proportions.

Examples

utils::data("example_scrnaseq" , package = "scFeatures")
data <- example_scrnaseq[1:50, 1:20]

celltype <- data$celltype
sample <- data$sample
data <- data@assays$RNA@data

alldata <- scFeatures:::formatData(data = data, celltype = celltype, sample = sample )

feature_proportion_raw <- run_proportion_raw(
    alldata,
    type = "scrna", ncores = 1
)

SydneyBioX/scFeatures documentation built on March 13, 2024, 12:36 a.m.