importPhyloseq {parafac4microbiome} | R Documentation |
Import Phyloseq object for PARAFAC modelling
Description
Import Phyloseq object for PARAFAC modelling
Usage
importPhyloseq(phyloseqObject, subjectIDs, thirdMode)
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)
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")
[Package parafac4microbiome version 1.0.3 Index]