find_biomarker {animalcules} | R Documentation |
Identify biomarkers
find_biomarker( MAE, tax_level, input_select_target_biomarker, nfolds = 3, nrepeats = 3, seed = 99, percent_top_biomarker = 0.2, model_name = c("logistic regression", "random forest") )
MAE |
A multi-assay experiment object |
tax_level |
The taxon level used for organisms |
input_select_target_biomarker |
Which condition is the target condition |
nfolds |
number of splits in CV |
nrepeats |
number of CVs with different random splits |
seed |
for repeatable research |
percent_top_biomarker |
Top importance percentage to pick biomarker |
model_name |
one of 'logistic regression', 'random forest' |
A list
data_dir = system.file('extdata/MAE.rds', package = 'animalcules') toy_data <- readRDS(data_dir) p <- find_biomarker(toy_data, tax_level='genus', input_select_target_biomarker=c('DISEASE'), nfolds = 3, nrepeats = 3, seed = 99, percent_top_biomarker = 0.2, model_name = 'logistic regression') p