inst/doc/CellDEEP_vignette.R

In CellDEEP: Cell DiffErential Expression by Pooling ('CellDEEP')

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

## ----load_data----------------------------------------------------------------
library(CellDEEP)
data("sim")

## -----------------------------------------------------------------------------
de.test <- FindMarker.CellDEEP(
  sim,
  group_id = "Status",
  sample_id = "DonorID",
  cluster_id = "cluster_id",
  Pool = TRUE,
  test.use = "wilcox",
  n_cells = 3,
  min_cells_per_subgroup = 1,
  cell_selection = "random",
  readcounts = "sum",
  logfc.threshold = 0.25,
  ident.1 = "Case",
  ident.2 = "Control"
)

## -----------------------------------------------------------------------------
pool_input <- prepare_data(
  sim,
  sample_id = "DonorID",
  group_id = "Status",
  cluster_id = "cluster_id"
)

## -----------------------------------------------------------------------------
pooled_kmean <- CellDEEP.Kmean(
  pool_input,
  readcounts = "sum",
  n_cells = 3,
  min_cells_per_subgroup = 1,
  assay_name = "RNA"
)
pooled_kmean

## -----------------------------------------------------------------------------
pooled_random <- CellDEEP.Random(
  pool_input,
  readcounts = "sum",
  n_cells = 5,
  min_cells_per_subgroup = 1,
  assay_name = "RNA"
)
pooled_random