check.confounders {SIAMCAT}R Documentation

Check for potential confounders in the metadata

Description

This function checks for associations between class labels and potential confounders (e.g. age, sex, or BMI) that are present in the metadata. Statistical testing is performed with Fisher's exact test or Wilcoxon test, while associations are visualized either as barplot or Q-Q plot, depending on the type of metadata. The conditional entropy evaluates associations among metadata variables and generalized linear models evaluate associations with the label, producing a correlation heatmap and appropriate quantitative barplots, respectively.

Usage

check.confounders(siamcat, fn.plot, meta.in = NULL, verbose = 1)

Arguments

siamcat

an object of class siamcat-class

fn.plot

string, filename for the pdf-plot

meta.in

vector, specific metadata variable names to analyze, defaults to NULL

verbose

control output: 0 for no output at all, 1 for only information about progress and success, 2 for normal level of information and 3 for full debug information, defaults to 1

Value

Does not return anything, but outputs plots to specified pdf file

Examples

    # Example data
    data(siamcat_example)

    # Simple working example
    check.confounders(siamcat_example, './conf_plot.pdf')


[Package SIAMCAT version 1.2.1 Index]