compare_daa_results: Compare the Consistency of Statistically Significant Features

In ggpicrust2: Make 'PICRUSt2' Output Analysis and Visualization Easier

Compare the Consistency of Statistically Significant Features

Description

This function compares the consistency and inconsistency of statistically significant features obtained using different methods in 'pathway_daa' from the 'ggpicrust2' package. It creates a report showing the number of common and different features identified by each method, and the features themselves.

Arguments

daa_results_list	A list of data frames containing statistically significant features obtained using different methods.
method_names	A character vector of names for each method used.
p_values_threshold	A numeric value representing the threshold for the p-values. Features with p-values less than this threshold are considered statistically significant. Default is 0.05.

Value

A data frame with the comparison results. The data frame has the following columns:

• method: The name of the method.

• num_features: The total number of statistically significant features obtained by the method.

• num_common_features: The number of features that are common to other methods.

• num_diff_features: The number of features that are different from other methods.

• diff_features: The names of the features that are different from other methods.

Examples

library(magrittr)
library(ggpicrust2)
library(tibble)
data("metacyc_abundance")
data("metadata")

# Run pathway_daa function for multiple methods
methods <- c("DESeq2", "edgeR","Maaslin2")
daa_results_list <- lapply(methods, function(method) {
pathway_daa(abundance = metacyc_abundance %>% column_to_rownames("pathway"),
metadata = metadata, group = "Environment", daa_method = method)
})

names(daa_results_list) <- methods
# Correct Maaslin2 feature names by replacing dots with hyphens.
# Note: When using Maaslin2 as the differential abundance analysis method,
# it modifies the original feature names by replacing hyphens (-) with dots (.).
# This replacement can cause inconsistencies when trying to compare results from Maaslin2
# with those from other methods that do not modify feature names.
# Therefore, this line of code reverses that replacement, converting the dots back into
# hyphens for accurate and consistent comparisons across different methods.
daa_results_list[["Maaslin2"]]$feature <- gsub("\\.", "-", daa_results_list[["Maaslin2"]]$feature)

# Compare results across different methods
comparison_results <- compare_daa_results(daa_results_list = daa_results_list,
method_names = c("DESeq2", "edgeR", "Maaslin2"))

ggpicrust2 documentation built on Nov. 8, 2023, 5:08 p.m.