Ref_free function

A reference-free deconvolution estimate

This function provides a reference-free deconvolution estimate, given a list of marker genes

Ref_free(bulk.data,list_marker,cell_type_unique,tol=0.001)

Arguments

• bulk.data: The ExpressionSet object for a target bulk data.
• list_marker: A list of pre-specified marker genes corresponding to each cell type.
• cell_type_unique: A list of cell types. It should match the order in list.marker.
• tol: A tolerance value for convergence. The default is 0.001.

Returns

The estimated cell type proportions, named est; and a goodness-of-fit value, named metrics. The smaller the better.

Examples

##read data
library(InteRD)
readRDSFromWeb<-function(ref) {readRDS(gzcon(url(ref)))}
urlremote<-"https://github.com/chencxxy28/Data/raw/main/data_InteRD/"
pseudo.seger<-readRDSFromWeb(paste0(urlremote,"pseudo.seger.rds"))
list_marker<-readRDSFromWeb(paste0(urlremote,"list_markerbaron20.rds"))
cell_type_unique<-c("alpha","beta","delta","gamma")
ref_free.output<-Ref_free(bulk.data=pseudo.seger,list_marker=list_marker,
cell_type_unique=cell_type_unique,tol=0.01) #make tol=0.001
reffree<-InteRD.predict.prop(InteRD.output=ref_free.output)