check.confounders {SIAMCAT} | R Documentation |
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.
check.confounders(siamcat, fn.plot, meta.in = NULL, verbose = 1)
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: |
Does not return anything, but outputs plots to specified pdf file
# Example data data(siamcat_example) # Simple working example check.confounders(siamcat_example, './conf_plot.pdf')