add.meta.pred: Add metadata as predictors

In zellerlab/siamcat: Statistical Inference of Associations between Microbial Communities And host phenoTypes

Add metadata as predictors

Description

This function adds metadata to the feature matrix to be later used as predictors

Usage

add.meta.pred(siamcat, pred.names, std.meta = TRUE, 
feature.type='normalized', verbose = 1)

Arguments

siamcat	object of class siamcat-class
pred.names	vector of names of the variables within the metadata to be added to the feature matrix as predictors
std.meta	boolean, should added metadata features be standardized?, defaults to TRUE
feature.type	string, on which type of features should the function work? Can be either "original", "filtered", or "normalized". Please only change this paramter if you know what you are doing!
verbose	integer, 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

Details

This functions adds one or several metadata variables to the set of features, so that they can be included for model training.

Usually, this function should be called before train.model.

Numerical meta-variables are added as z-scores to the feature matrix unless specified otherwise.

Please be aware, that non-numerical metadata variables will be converted to numerical values by using as.numeric() and could therefore lead to errors. Thus, it makes sense to encode non-numerical metadata variables to numerically before you start the SIAMCAT workflow.

Value

an object of class siamcat-class with metadata added to the features

Examples

data(siamcat_example)

# Add the Age of the patients as potential predictor
siamcat_age_added <- add.meta.pred(siamcat_example, pred.names=c('Age'))

# Add Age and BMI as potential predictors
# Additionally, prevent standardization of the added features
siamcat_meta_added <- add.meta.pred(siamcat_example, 
    pred.names=c('Age', 'BMI'), std.meta=FALSE)

zellerlab/siamcat documentation built on Feb. 1, 2024, 2:21 a.m.