import_picrust2: Import function to read the output of picrust2 as phyloseq...

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

Import function to read the output of picrust2 as phyloseq object

Description

Import the output of picrust2 into phyloseq object

Usage

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".

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.

Value

phyloseq::phyloseq object.

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

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.