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.

### 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)

[Package SIAMCAT version 1.0.0 Index]