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# Wilcoxon test to compare cell population frequencies

Source: `R/differential_testing.R`
`frequency_wilcox_test.Rd`

`frequency_wilcox_test()` performs a two-sided, two-sample Wilcoxon Rank Sum test (independent) or Wilcoxon Signed Rank test (paired data) on cell type frequencies.

## Usage

    frequency_wilcox_test(
      fcd,
      cluster_slot,
      cluster_var,
      sample_var,
      group_var,
      pair_var = NULL,
      paired_test = F,
      p.adjust.method = "bonferroni",
      detailed = F,
      numeric = F,
      print_results = T
    )

## Arguments

fcd

  flow cytometry data set, that has been subjected to clustering or cell type label prediction with cyCONDOR

cluster_slot

  string specifying which clustering slot to use to find variable specified in cluster_var

cluster_var

  string specifying variable in cluster_slot that identifies cell population labels to be used (e.g. clusters, metaclusters or predicted labels).

sample_var

  string indicating variable in cell_anno that defines sample IDs to be used.

group_var

  string indicating variable in cell_anno that should be used to group samples in sample_var. group_var must have exactly two levels.

pair_var

  string indicating variable in cell_anno that defines pairing of samples, e.g. donor ID, that should be used if `paired_test = T`.

paired_test

  logical, indicating if a paired (TRUE) or unpaired test (FALSE, default) should be performed.

p.adjust.method

  p-value adjustment method to use for multiple comparison testing, e.g "bonferroni" (default) or "BH" (Benjamini-Hochberg). All available options can be checked in the documentation of the `adjust_pvalue` function from the package `rstatix`.

detailed

  logical if detailed output from `wilcox_test` should be reported.

numeric

  logical, if TRUE numeric levels in cluster_var are ordered in ascending order and "Cluster_" is pasted before number, if FALSE alphabetical ordering is applied.

print_results

  Logical, indicating if the test results are printed to the console (TRUE) or not (FALSE).

## Value

`frequency_wilcox_test` returns the fcd containing a data frame produced by `wilcox_test` with two additional columns, "cluster" containing the information, which cell population was tested, and "applied_test", indicating which test was used. Results are stored in the fcd under extras$statistics.

## Details

frequency_wilcox_test

`frequency_wilcox_test()` is a wrapper function around the `wilcox_test()` function implemented in the package `rstatix`. The function first calculates cell population frequencies for each sample in sample_var. Then a two-sided, two sample wilcoxon test is performed between two groups defined in group_var. The test can either be run unpaired (two independent groups) or paired. Afterwards, p-value adjustment will be performed across all comparisons that were made.