processDataCube {parafac4microbiome} | R Documentation |
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
)
Arguments
dataset |
A longitudinal microbiome dataset, formatted as follows:
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 |
scaleMode |
Mode to scale within: 1=subjects,2=features,3=time (default 0, i.e. do not scale). See |
Value
CLRed, centered and scaled cube
Examples
processedCube = processDataCube(Fujita2023)