Friedman Rank Sum test to compare cell population frequencies of paired samples

frequency_friedman_test() performs a Friedman Rank Sum test to compare cell population frequencies of three of more groups. Optionally, post-hoc testing is performed using Wilcoxon Rank Sum test.

Usage

frequency_friedman_test(
  fcd,
  cluster_slot,
  cluster_var,
  sample_var,
  group_var,
  pair_var,
  friedman_p.adjust.method = "bonferroni",
  numeric = F,
  post_hoc_test = F,
  post_hoc_p.adjust.method = "bonferroni",
  friedman_sig_threshold = 0.05
)

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 three or more levels.

pair_var

string indicating variable in cell_anno that should be used to pair the samples.

friedman_p.adjust.method

p-value adjustment method to use for multiple comparisons of Friedman Rank Sum test, 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.

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.

post_hoc_test

logical, whether to perform post-hoc testing (TRUE, default) or not (FALSE).

post_hoc_p.adjust.method

p-value adjustment method to use for post-hoc testing, e.g "bonferroni" (default). All available options can be checked in the documentation of the adjust_pvalue function from the package rstatix.

friedman_sig_threshold

significance threshold Friedman Rank Sum test. For all Friedman Rank Sum comparisons with an adjusted p-value equal or smaller than the threshold, post-hoc tests are performed (default 0.05)

Value

frequency_friedman_test returns a list of two data frames, "friedman_test" and "wilcox_test". "friedman_test" comprises results produced by friedman_test and friedman_effsize and "wilcox_test" contains results obtained by wilcox_test. Both data frames have one additional columns, "cluster", containing the information, which cell population was tested.

Details

frequency_friedman_test

frequency_friedman_test() is a wrapper function around friedman_test, friedman_effsize and wilcox_test implemented in the package rstatix. The function first calculates cell population frequencies for each sample in sample_var. Then a Friedman Rank Sum test is performed for each cell population followed by p-value adjustment. If post_hoc = T, post-hoc testing with pairwise Wilcoxon Rank Sum Tests and p-value correction is performed for each significant Friedman Rank Sum test comparison.