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)
siamcat | an object of class siamcat-class |
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fn.plot | string, filename for the pdf-plot |
verbose | control output: |
Does not return anything, but produces a single plot for each metadata category.
# 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) # }