Process a multi-way array of count data.
Usage
processDataCube(
dataset,
sparsityThreshold = 1,
considerGroups = FALSE,
groupVariable = "",
CLR = TRUE,
centerMode = 0,
scaleMode = 0
)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.