melonnpan.train: Model-based Genomically Informed High-dimensional Predictor...

Description Usage Arguments

View source: R/melonnpan_train.R

Description

Predict metabolites from microbial sequence features' abundances. Both measurements are expected to be normalized before using MelonnPan and so are proportional data ranging from 0.0 to 1.0.

Usage

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melonnpan.train(
  metab = metab,
  metag = metag,
  alpha = seq(0.05, 0.95, 0.05),
  lambda.choice = "lambda.1se",
  nfolds = 10,
  correction = "fdr",
  method = "spearman",
  cores = 4,
  seed = 1234,
  cutoff = 0.05,
  verbose = TRUE,
  plot = FALSE,
  outputString = c("MelonnPan_Training_Summary", "MelonnPan_Trained_Weights",
    "MelonnPan_Trained_Metabolites"),
  outputDirectory = paste(getwd(), "/", sep = "")
)

Arguments

metab

Training data of metabolite relative abundances. Must have the exact same rows (subjects/samples) as metag.

metag

Training data of sequence features' relative abundances. Must have the exact same rows (subjects/samples) as metab.

alpha

Grid of alpha values between 0 and 1. Default is 'seq(0.05, 0.95, 0.05)'.

lambda.choice

Choice of optimal lambda ('lambda.min' or 'lambda.1se'). Default is 'lambda.1se'.

nfolds

Number of folds for internal cross-validation. Default is 10.

correction

Multiplicity adjustment method, same as 'p.adjust'. Default is 'fdr'.

method

Method to correlate measured and predicted metabolites ('spearman' or 'pearson'). Default is 'spearman'.

cores

Number of cores to use for parallel processing. Default is 4.

seed

Specify the arbitrary seed value for reproducibility. Default is 1234.

cutoff

Q-value threshold for significant prediction. Default is 0.05.

verbose

Should detalied message be printed. Default is TRUE.

plot

Should CV error as a function of lambda be plotted. Default is FALSE.

outputString

Names of the three output files. Default is 'MelonnPan_Training_Summary', 'MelonnPan_Trained_Weights', and 'MelonnPan_Trained_Metabolites'.

outputDirectory

Name of the desired output directory. Default is the current directory.


biobakery/melonnpan documentation built on May 17, 2021, 3:27 a.m.