In LeoStafu/metaDAF: Metagenomics tools for detecting Differentially Abundant Features

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

rm(list = ls())
library(metaDAF)
library(tidyverse)
data("QinJ_2012_metadata")
data("QinJ_2012_table_count")
load("../R/sysdata.rda")

Repetitions

Here is the same analysis repeated several times :

dataTest_double <- generate_repeated_DAF_data(times = 5,
                                              count_table = QinJ_2012_table_count,
                                              metadata = QinJ_2012_metadata)
res2 <- run_DAF_analysis(data = dataTest_double, method = "deseq2")
plot_data2 <- generate_curve_data(dt = res2,
                                 threshold_var = "adjusted_pvalue")
curve_plot(curve_data = plot_data2, type = "roc",
           plot_title = "Example of DESeq2 run - 5 times")

Comparions of several methods

Or if one want to compare multiple methods together :

curve_plot(curve_data = res_test_compare_rep_plot_data, type = "roc",
           plot_title = "Example of methods comparison")
boxplot_AUC(curve_data = res_test_compare_rep_plot_data, auc_limit = 1)


curve_plot(curve_data = res_test_compare_rep_plot_data, type = "roc",
           plot_title = "Example of methods comparison") + coord_cartesian(xlim = c(0, 0.1))

LeoStafu/metaDAF documentation built on July 14, 2019, 6:41 p.m.