get_Components {MMINP}

Estimate components for O2-PLS method

Description

get components number using Cross-validate procedure of O2-PLS

Usage

get_Components(
  metag,
  metab,
  compmethod = NULL,
  n = 1:10,
  nx = 0:5,
  ny = 0:5,
  seed = 1234,
  nr_folds = 3,
  nr_cores = 1
)

Arguments

metag

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

metab

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

compmethod

A character string indicating which Cross-validate procedure of O2PLS is to be used for estimating components, must be one of "NULL", "cvo2m" or "cvo2m.adj". If set to "NULL", depends on the features number.

n

Integer. Number of joint PLS components. Must be positive. More details in crossval_o2m and crossval_o2m_adjR2.

nx

Integer. Number of orthogonal components in metag. Negative values are interpreted as 0. More details in crossval_o2m and crossval_o2m_adjR2.

ny

Integer. Number of orthogonal components in metab. Negative values are interpreted as 0. More details in crossval_o2m and crossval_o2m_adjR2.

seed

a random seed to make the analysis reproducible, default is 1234.

nr_folds

Positive integer. Number of folds to consider. Note: kcv=N gives leave-one-out CV. Note that CV with less than two folds does not make sense. More details in crossval_o2m and crossval_o2m_adjR2.

nr_cores

Positive integer. Number of cores to use for CV. You might want to use detectCores(). Defaults to 1. More details in crossval_o2m and crossval_o2m_adjR2.

Value

A data frame of components number