importMicrobiotaProcess: Import MicrobiotaProcess object for PARAFAC modelling

In parafac4microbiome: Parallel Factor Analysis Modelling of Longitudinal Microbiome Data

Import MicrobiotaProcess object for PARAFAC modelling

Description

Import MicrobiotaProcess object for PARAFAC modelling

Usage

importMicrobiotaProcess(MPobject, subjectIDs, thirdMode, taxa_are_rows = TRUE)

Arguments

MPobject	MicrobiotaProcess object containing at least an OTU table and sample information, preferably also taxonomic information.
subjectIDs	Column name in the sample information corresponding to the subject IDs.
thirdMode	Column name in the sample information corresponding to the study design aspect to put in the third mode of the data cube.
taxa_are_rows	Boolean specifying if the taxa are in the rows of the OTU table (TRUE) or not (FALSE).

Value

List object containing:

• 'data': data cube

• 'mode1': metadata of the subject mode

• 'mode2': taxonomy information

• 'mode3': metadata of the third mode

Examples

## Not run: 
library(MicrobiotaProcess)
data("mouse.time.mpse")
importMicrobiotaProcess(mouse.time.mpse, subjectIDs = "Sample",
                        thirdMode = "time", taxa_are_rows = TRUE)

## End(Not run)

parafac4microbiome documentation built on June 8, 2025, 11:40 a.m.