metaprotr (version 1.2.2)

add_taxonomy: add_taxonomy

Description

Integrates the database containing the taxonomic classification of the identified proteins in a "metaproteome_object". The taxonomic classification is previously obtained by aligment algorithms and must include seven taxonomic levels assigned to a given protein: species, genus, family, order, class, phylum and superkingdom

Usage

add_taxonomy(metaproteome_object, taxonomic_database)

Arguments

metaproteome_object

List defined as "metaproteome_object" containing proteins and peptides abundances. The format of this object is similar to that generated from the function "load_protspeps".

taxonomic_database

Dataframe containing the taxonomic information for each protein. The first column must contain the same identifiers of those present in the column "Accession" from the dataframe "peptides_proteins" of the "metaproteome_object". Two additional columns have to be present: i) one named "organism" containing the name of the strain assigned to a given protein; and ii) the other named "species.genus.family.order.class.phylum.superkingdom". The taxonomic classification can be obtained from a tool of sequences aligment and must be ordered as follows: species, genus, family, order, class, phylum and superkingdom. The characters inside must be concatenated by a comma (ex."Streptococcus anginosus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Firmicutes,Bacteria"). An example can be found in this repository.

Value

A "metaproteome_object", which is a list of six elements with format similar to that generated from the function "load_protspeps". An additional column containing the taxonomic annotation is added to the dataframe named "peptides_proteins".

Examples

# NOT RUN {
# Download taxonmical annotation db: https://zenodo.org/record/3997093#.X0UYI6Zb_mE 
meta99_full_taxo <- read.csv2("MetaHIT99_best_hit_taxo_complete.tsv", header = TRUE, sep="\t") 

# Files with spectral abundance and proteins list from X!Tandempipeline
protein_file <- "your/specific/location/protein_list.txt"
peptide_file <- "your/specific/location/peptide_counting.txt"
metadata_file <- "your/location/metadata.csv"

metaproteome <- load_protspeps(proteins_file, peptides_file, metadata_file)

metaproteome_taxo <- add_taxonomy(metaproteome, meta99_full_taxo) 

# }