Calculate DGE between two cell groups — find_markers

This function can be used to calculate differentially expressed genes between two groups in the single cell data. At the moment, it has only an implementation for the Wilcox-based rank statistic.

Usage

find_markers_sc(
  object,
  cells_1,
  cells_2,
  method = c("wilcox"),
  alternative = c("twosided", "greater", "less"),
  min_prop = 0.05,
  .verbose = TRUE
)

Arguments

object: SingleCells class.
cells_1: String. The names of the cells in group 1. Need to be part of the cell names in the object, see get_cell_names().
cells_2: String. The names of the cells in group 2. Need to be part of the cell names in the object, see get_cell_names().
method: String. Which method to use for the calculations of the DGE. At the moment the only option is "wilcox", but the parameter is reserved for future features.
alternative: String. Test alternative. One of c("twosided", "greater", "less"). Function will default to "twosided".
min_prop: Numeric. The minimum proportion of cells that need to express the gene to be tested in any of the two groups.
.verbose: Boolean. Controls verbosity of the function.

Value

data.table with the DGE results from the test.