generateBulk: bulk data generation function

In chencxxy28/MultiRD: Multi-robust deconvolution algorithm

Description

Construct Pseudo bulk samples by random sampled number of cells per subject, but based on the actual numbers.

Usage

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

Arguments

eset	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	number of pseudo bulk samples to be constructed
samplewithRep	logical, randomly sample single cells with replacement. Default is F.
low_s	lower supprot a for uniform distribution U[a,b]
upp_s	upper supprot b for uniform distribution U[a,b]

Value

pseudo bulk samples ExpressionSet, and actual cell-type proportions

chencxxy28/MultiRD documentation built on Dec. 19, 2021, 3:03 p.m.