importTreeSummarizedExperiment {parafac4microbiome} | R Documentation |
Import TreeSummarizedExperiment object for PARAFAC modelling
Description
Import TreeSummarizedExperiment object for PARAFAC modelling
Usage
importTreeSummarizedExperiment(
treeObject,
subjectIDs,
thirdMode,
taxa_are_rows
)
Arguments
treeObject |
TreeSummarizedExperiment object containing at least an OTU table and sample information, preferably also taxonomic information. |
subjectIDs |
Column name in the sample information corresponding to the subject IDs. |
thirdMode |
Column name in the sample information corresponding to the study design aspect to put in the third mode of the data cube. |
taxa_are_rows |
Boolean specifying if the taxa are in the rows of the OTU table (TRUE) or not (FALSE). |
Value
List object containing:
'data': data cube
'mode1': metadata of the subject mode
'mode2': taxonomy information
'mode3': metadata of the third mode
Examples
library(TreeSummarizedExperiment)
fakeOTU = t(rTensor::k_unfold(rTensor::as.tensor(Fujita2023$data), 2)@data)
fakeTaxa = as.matrix(Fujita2023$mode2)
fakeSam = as.data.frame(cbind(rep(1:8, 110), rep(1:110, each=8)))
colnames(fakeSam) = c("replicate.id", "timepoint")
fakeTreeObj = TreeSummarizedExperiment(assays = list(Count = fakeOTU),
rowData = fakeSam,
colData = fakeTaxa)
dataset = importTreeSummarizedExperiment(fakeTreeObj,
subjectIDs="replicate.id",
thirdMode="timepoint",
taxa_are_rows=FALSE)
[Package parafac4microbiome version 1.0.3 Index]