Import function to read the output of picrust2 as phyloseq object

Source: R/import-picrust2.R

Import the output of picrust2 into phyloseq object

import_picrust2(
  feature_tab,
  sam_tab = NULL,
  trait = c("PATHWAY", "COG", "EC", "KO", "PFAM", "TIGRFAM", "PHENO")
)

Arguments

feature_tab

character, file path of the prediction abundance table of functional feature.

sam_tab

character, file path of the sample meta data.

trait

character, options are picrust2 function traits (including "COG", "EC", "KO", "PFAM", "TIGRFAM", and "PHENO") and "PATHWAY".

Value

phyloseq::phyloseq object.

Details

PICRUSt2 is a software for predicting abundances of functional profiles based on marker gene sequencing data. The functional profiles can be predicted from the taxonomic profiles using PICRUSt2. "Function" usually refers to gene families such as KEGG orthologs and Enzyme Classification numbers, but predictions can be made for any arbitrary trait.

In the phyloseq object, the predicted function abundance profile is stored in otu_table slot. And the functional trait is saved in tax_table slot, if the descriptions of function features is not added to the predicted table, tax_table will have only one rank Picrust_trait to represent the function feature id, or if the desciptions are added one more rank Picrust_description will be added to represent the description of function feature.

Examples

sam_tab <- system.file(
    "extdata", "picrust2_metadata.tsv",
    package = "microbiomeMarker")
feature_tab <- system.file(
    "extdata", "path_abun_unstrat_descrip.tsv.gz",
    package = "microbiomeMarker")
ps <- import_picrust2(feature_tab, sam_tab, trait = "PATHWAY")
ps
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 195 taxa and 24 samples ]
#> sample_data() Sample Data:       [ 24 samples by 3 sample variables ]
#> tax_table()   Taxonomy Table:    [ 195 taxa by 2 taxonomic ranks ]