generateBulk_norep: Construct Pseudo bulk samples - random

In meichendong/SCDC: Bulk RNA-seq deconvolution by scRNA-seq with multi-reference datasets

Construct Pseudo bulk samples – random

Description

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

Usage

generateBulk_norep(
  eset,
  ct.varname,
  sample,
  disease = NULL,
  ct.sub,
  prop_mat = NULL,
  nbulk = 10,
  samplewithRep = F
)

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.

Value

pseudo bulk samples ExpressionSet, and actual cell-type proportions

meichendong/SCDC documentation built on Jan. 26, 2023, 5:08 p.m.