Wilcoxon test to compare cell population frequencies

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
)

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.

Value

frequency_wilcox_test returns 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.

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.