check.confounders {SIAMCAT} | R Documentation

## Check for potential confounders in the metadata

### Description

Checks potential confounders in the metadata and produces some visualizations

### Usage

    check.confounders(siamcat, fn.plot, meta.in = NULL,
    feature.type='filtered', 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 (all metadata variables will be analyzed)
`feature.type` | string, on which type of features should the function work? Can be either `c()"original", "filtered", or "normalized")`. Please only change this paramter if you know what you are doing!
`verbose` | integer, 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`

### Details

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.

Additionally, it evaluates associations among metadata variables using conditional entropy and associations with the label using generalized linear models, producing a correlation heatmap and appropriate quantitative barplots, respectively.

### 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 1.12.0 Index]