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Calculate DGE between two cell groups

find_markers_sc.Rd

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 or SingleCellsSubset 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 or integer. Controls verbosity and returns run times. FALSE -> quiet, TRUE or 1L -> normal verbosity, 2L -> detailed verbosity.

Value

data.table with the DGE results from the test.

Examples

# Wilcoxon test between two of the planted cell types
sc <- demo_single_cells()
obs <- get_sc_obs(sc)
res <- find_markers_sc(
  sc,
  cells_1 = obs$cell_id[obs$cell_grp == "cell_type_1"],
  cells_2 = obs$cell_id[obs$cell_grp == "cell_type_2"],
  .verbose = FALSE
)
head(res)
#>    gene_id      lfc     prop1     prop2 z_scores     p_values          fdr
#>     <char>    <num>     <num>     <num>    <num>        <num>        <num>
#> 1: gene_01 3.339259 0.9880239 0.6946108 14.38283 6.632426e-47 7.043991e-46
#> 2: gene_02 3.292560 0.9880239 0.6886228 14.16134 1.589201e-45 9.932503e-45
#> 3: gene_03 3.461920 1.0000000 0.6946108 14.95929 1.354582e-50 3.386456e-49
#> 4: gene_04 2.915536 0.9580838 0.6886228 12.95389 2.233137e-38 8.588988e-38
#> 5: gene_05 2.709311 0.8383234 0.4431138 10.68923 1.142846e-26 3.361312e-26
#> 6: gene_06 3.113609 0.9760479 0.7005988 14.03355 9.715047e-45 5.397248e-44

unlink(sc@dir_data, recursive = TRUE, force = TRUE)