pop.ct.prop.scRNA {InteRD} | R Documentation |
Calculate the population-level cell type proportions from a single-cell data.
Description
Calculate population-level cell type proportions from single-cell data.
Usage
pop.ct.prop.scRNA(scRNA,cluster="cluster",sample="sample",cell_type_unique)
Arguments
scRNA |
The 'ExpressionSet' object for single-cell data. |
cluster |
The character string specifying the variable name for cell types. The default is "cluster". |
sample |
The character string specifying the variable name for subject/samples. The default is "sample". |
cell_type_unique |
A vector of cell types. It should match the order in list.marker. |
Value
The population-level cell type proportions ('pop.ct.prop') and corresponding standard deviations ('pop.ct.sd').
Examples
##read data
library(InteRD)
readRDSFromWeb<-function(ref) {readRDS(gzcon(url(ref)))}
urlremote<-"https://github.com/chencxxy28/Data/raw/main/data_InteRD/"
seger<-readRDSFromWeb(paste0(urlremote,"segerstolpe.rds"))
cell_type_unique<-c("alpha","beta","delta","gamma")
ave_est<-pop.ct.prop.scRNA(scRNA=seger[["sc.eset.qc"]],
cell_type_unique=cell_type_unique)$pop.ct.prop
ave_est
[Package InteRD version 0.1.1 Index]