parafac4microbiome (version 1.1.2)

processDataCube: Process a multi-way array of count data.

Description

Process a multi-way array of count data.

Usage

processDataCube(
  dataset,
  sparsityThreshold = 1,
  considerGroups = FALSE,
  groupVariable = "",
  CLR = TRUE,
  centerMode = 0,
  scaleMode = 0
)

Value

CLRed, centered and scaled cube

Arguments

dataset

A longitudinal microbiome dataset, formatted as follows:

data

Array object of the data cube filled with counts

mode1

Dataframe with all the subject metadata, 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 array.

See Fujita2023, Shao2019 or vanderPloeg2024 for more information.

sparsityThreshold

Maximum sparsity for a feature to be selected (default=1, i.e. do not select features).

considerGroups

Consider groups when calculating sparsity (default=FALSE).

groupVariable

Column name in dataset$mode1 that should be used to consider groups (default="").

CLR

Perform a centered log-ratio transformation of the count data (default=TRUE).

centerMode

Mode to center across: 1=subjects,2=features,3=time (default 0, i.e. do not center). See multiwayCenter() for more information.

scaleMode

Mode to scale within: 1=subjects,2=features,3=time (default 0, i.e. do not scale). See multiwayScale() for more information.

Examples

processedCube = processDataCube(Fujita2023)