find_biomarker: Identify biomarkers

In animalcules: Interactive microbiome analysis toolkit

Description

Identify biomarkers

Usage

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")
)

Arguments

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'

Value

A list

Examples

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

animalcules documentation built on Nov. 8, 2020, 6:47 p.m.