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.

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')
#> Error in label$p.idx: $ operator not defined for this S4 class
# Additional information with verbose
# NOT RUN { check.confounders(siamcat_example, './conf_plot.pdf', verbose=2) # }