generateBulk function

Pseudo bulk data generation function

This function generates a pseudo bulk samples by random sampled number of cells per subject.

generateBulk(eset,ct.varname,sample,disease = NULL,ct.sub,prop_mat = NULL,
nbulk = 50,samplewithRep = FALSE,low_s = 0.3,upp_s = 0.7)

Arguments

• eset: The ExpressionSet object for single cells.
• ct.varname: Variable name for 'cell types'.
• sample: Variable name for subject/samples.
• disease: Indicate the health condition of subjects.
• ct.sub: A subset of cell types that are selected to construct pseudo bulk samples. If NULL, then all cell types are used.
• prop_mat: Manually input the cell-type proportion for pseudo bulk samples.
• nbulk: The number of pseudo bulk samples to be constructed.
• samplewithRep: Logical, randomly sample single cells with replacement. Default is F.
• low_s: Lower support a for uniform distribution U[a,b].
• upp_s: Upper support b for uniform distribution U[a,b].

Returns

Pseudo bulk samples in the format of ExpressionSet, and the true cell-type proportions.

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"))

##generate a pseudo bulk data with two samples
set.seed(1234567)
pseudo.seger<-generateBulk(seger[["sc.eset.qc"]], ct.varname = "cluster",
sample = "sample", ct.sub = c("alpha","beta","delta","gamma"),
nbulk = 2, low_s = 0.3, upp_s = 0.7)