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.
Arguments
- data
A list object containing
data
matrix andcelltype
andsample
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
)