Import Phyloseq object for PARAFAC modelling
Arguments
- phyloseqObject
Phyloseq object containing at least an otu table and sample data, preferably also taxonomic information.
- subjectIDs
Column name in sam_data corresponding to the subject IDs.
- thirdMode
Column name in sam_data corresponding to the study design aspect to put in the third mode of the data cube.
Value
List object containing:
'data': data cube
'mode1': metadata of the subject mode
'mode2': taxonomy information
'mode3': metadata of the third mode
Examples
library(phyloseq)
#>
#> Attaching package: ‘phyloseq’
#> The following object is masked from ‘package:MicrobiotaProcess’:
#>
#> tax_table
data(GlobalPatterns)
GP = GlobalPatterns
# Add custom subject IDs to the sample data to make this example work
alteredSampleData = sample_data(GP)
alteredSampleData$subjectID = c(1,2,3,1,2,1,2,3,1,2,1,2,1,2,3,1,2,3,1,2,3,4,5,1,2,3)
df = phyloseq(otu_table(GP), tax_table(GP), alteredSampleData)
# Make a data cube with SampleType (soil, feces, etc.) as the third mode.
result = importPhyloseq(df, subjectIDs = "subjectID", thirdMode="SampleType")