reshapeData: Reorganize longitudinal microbiome into a data cube ready for...

In parafac4microbiome: Parallel Factor Analysis Modelling of Longitudinal Microbiome Data

Reorganize longitudinal microbiome into a data cube ready for PARAFAC modelling.

Description

Reorganize longitudinal microbiome into a data cube ready for PARAFAC modelling.

Usage

reshapeData(
  Xlong,
  subjectMetadata,
  featureMetadata,
  timepointMetadata,
  timepointOrder = sort(unique(timepointMetadata))
)

Arguments

Xlong	Longitudinal microbiome count data in matrix (long) format.
subjectMetadata	Vector containing the subjects corresponding to the measurements in Xlong.
featureMetadata	Taxonomic classification of the microbiota, ordered the same as the columns in Xlong.
timepointMetadata	Vector containing the time points corresponding to the measurements in Xlong.
timepointOrder	Vector containing the required order of the timepoints in timepointMetadata (default: sort(unique(timepointMetadata)) ).

Value

#' A list object containing

data

Array object of the data cube

mode1

Dataframe with the subjects, ordered the same as the rows in the data cube.

mode2

Taxonomic classification of the microbiota, ordered the same as the columns in the data cube.

mode3

Dataframe with the time metadata, ordered the same as the third dimension in the data cube.

...

Examples

library(dplyr)

Xlong = array(rnorm(108*5*10), c(108*5, 10))
subjects = rep(1:108, 5)
features = rep(1:10)
timepoints = rep(1:5, each=108)

dataset = reshapeData(Xlong, subjects, features, timepoints)

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