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Bulk_generator

Bulk_generator() function returns a list containing two data.frame :

  • T the Num.mixtures mixtures
  • P the proportions used to build T

Instalation

if(!require(devtools)){install.packages("devtools")}
devtools::install_github("adrien0598/bulkfakr")

Quick use

# sc_counts a single cell dataset
# phenoData a data.frame with information about matching cellType and cellID

pseudoBulk <- Bulk_generator(sc_counts, phenoData)
pseudoBulk$T #mixtures
pseudoBulk$P #proportions

Cells in sc_counts that did not match with phenoData cellID will not be used. If no match or only one cellType, execution will be stopped.

Remove cells from phenoData

pseudoBulk <- Bulk_generator(sc_counts, phenoData, forbidden_CT = c("cell_type1","cell_type2"))

pseudoBulk$T #mixtures
pseudoBulk$P #proportions, cell_type1 and cell_types2 will be 0 for all mixtures

Force all cell types in all mixtures

pseudoBulk <- Bulk_generator(sc_counts, phenoData, nb_CT_random = FALSE)

pseudoBulk$T #mixtures
pseudoBulk$P #proportions, no 0 (except rounded ones)

Other parameters

  • Num.mixtures = 1000
  • pool.size = 100
  • min.percentage = 1
  • max.percentage = 99
  • seed = 24