run_proportion_ratio: Generate cell type proportion ratio

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

Generate cell type proportion ratio

Description

This function calculates pairwise cell type proportion ratio for each sample. and applies a logit transformation to the proportions. 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_ratio(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 vs celltype b, celltype a vs celltype c, with the number representing the ratio between the two cell types.

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_ratio <- run_proportion_ratio(
    alldata,
    type = "scrna", ncores = 1
)

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