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Batch Wilcoxon Rank-Sum Test Between Two Groups

Source: R/batch_wilcoxon.R
batch_wilcoxon.Rd

Performs Wilcoxon rank-sum tests (Mann-Whitney U tests) to compare the distribution of specified features between two groups. Computes p-values, adjusts for multiple testing, and ranks features by significance.

Usage

batch_wilcoxon(
  data,
  target = "group",
  feature = NULL,
  feature_manipulation = FALSE
)

Arguments

data

Data frame containing the dataset for analysis.

target

Character string specifying the column name of the grouping variable. Default is `"group"`.

feature

Character vector specifying feature names to analyze. If `NULL`, prompts for selection (interactive mode only). Default is `NULL`.

feature_manipulation

Logical indicating whether to apply feature manipulation filtering. Default is `FALSE`.

Value

Tibble with columns:

sig_names

Feature name

p.value

Raw p-value

statistic

Difference in means between groups

p.adj

Adjusted p-value (Benjamini-Hochberg)

log10pvalue

Negative log10-transformed p-value

stars

Significance stars: **** p<0.0001, *** p<0.001, ** p<0.01, * p<0.05, + p<0.5

group1, group2

Mean values for each group

Author

Dongqiang Zeng

Examples

# Load TCGA-STAD signature data
sig_stad <- load_data("sig_stad")

# Compare features by gender
res <- batch_wilcoxon(
  data = sig_stad,
  target = "Gender",
  feature = colnames(sig_stad)[69:ncol(sig_stad)]
)
#> ℹ Groups: "M" and "F"
#> ℹ Features: 255
#> ✔ Wilcoxon test complete
head(res)
#> # A tibble: 6 × 8
#>   sig_names               p.value      F     M statistic p.adj log10pvalue stars
#>   <chr>                     <dbl>  <dbl> <dbl>     <dbl> <dbl>       <dbl> <fct>
#> 1 Steroid_Hormone_Metabo… 0.00653 -0.526 0.292    -0.818 0.717        2.18 **   
#> 2 Steroid_Hormone_Biosyn… 0.00694 -0.516 0.284    -0.800 0.717        2.16 **   
#> 3 Linoleic_Acid_Metaboli… 0.00991 -0.345 0.192    -0.537 0.717        2.00 **   
#> 4 Ascorbate_and_Aldrate_… 0.0112  -0.371 0.204    -0.575 0.717        1.95 *    
#> 5 Pentose_and_Glucuronat… 0.0189  -0.378 0.210    -0.588 0.854        1.72 *    
#> 6 Drug_Metabolism_by_Cyt… 0.0201  -0.548 0.295    -0.843 0.854        1.70 *