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]