Import MicrobiotaProcess object for PARAFAC modelling

Usage

importMicrobiotaProcess(MPobject, subjectIDs, thirdMode, taxa_are_rows = TRUE)

Arguments

MPobject: MicrobiotaProcess 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

# \donttest{
library(MicrobiotaProcess)
#> MicrobiotaProcess v1.16.1 For help:
#> https://github.com/YuLab-SMU/MicrobiotaProcess/issues
#> 
#> If you use MicrobiotaProcess in published research, please cite the
#> paper:
#> 
#> Shuangbin Xu, Li Zhan, Wenli Tang, Qianwen Wang, Zehan Dai, Lang Zhou,
#> Tingze Feng, Meijun Chen, Tianzhi Wu, Erqiang Hu, Guangchuang Yu.
#> MicrobiotaProcess: A comprehensive R package for deep mining
#> microbiome. The Innovation. 2023, 4(2):100388. doi:
#> 10.1016/j.xinn.2023.100388
#> 
#> Export the citation to BibTex by citation('MicrobiotaProcess')
#> 
#> This message can be suppressed by:
#> suppressPackageStartupMessages(library(MicrobiotaProcess))
#> 
#> Attaching package: ‘MicrobiotaProcess’
#> The following object is masked from ‘package:stats’:
#> 
#>     filter

# Generate synthetic data
sample_info = data.frame(Sample = factor(c("S1", "S2", "S3", "S4", "S5")),
                         time = factor(c("T1", "T2", "T1", "T2", "T1")))
otu_table = matrix(runif(25, min = 0, max = 100), nrow = 5, ncol = 5,
                   dimnames = list(paste0("OTU", 1:5), sample_info$Sample))

taxonomy_table = data.frame(OTU = paste0("OTU", 1:5),
                            Kingdom = rep("King", 5),
                            Phylum = rep("Phy", 5),
                            Class = rep("Cla", 5),
                            Order = rep("Ord", 5),
                            Family = rep("Fam", 5),
                            Genus = rep("Gen", 5))

# Create Summarized Experiment
synthetic_SE = SummarizedExperiment::SummarizedExperiment(
               assays = list(otu = otu_table),
               colData = sample_info,
               rowData = taxonomy_table)

# Convert to MicrobiotaProcess object
synthetic_MPSE = as.MPSE(synthetic_SE)

dataset = importMicrobiotaProcess(synthetic_MPSE,
                                  subjectIDs = "Sample",
                                  thirdMode = "time",
                                  taxa_are_rows = TRUE)
# }