parafac4microbiome (version 1.2.1)

reshapeData: 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))
)

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.

...

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)) ).

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)