check.confounders: Check for potential confounders in the metadata

In KonradZych/SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes

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.

Usage

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

Arguments

siamcat	an object of class siamcat-class
fn.plot	string, filename for the pdf-plot
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 produces a single plot for each metadata category.

Examples

    # Example data
    data(siamcat_example)
    # since the whole pipeline has been run in the example data, exchange the
    # normalized features with the original features
    siamcat_example <- reset.features(siamcat_example)

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

    # Additional information with verbose
    ## Not run: 
    check.confounders(siamcat_example, './conf_plot.pdf', 
    verbose=2)
## End(Not run)

KonradZych/SIAMCAT documentation built on May 17, 2019, 6:20 p.m.