mpa2meco: Transform metagenomic classification results of 'mpa' format...

In file2meco: Transform Files to 'microtable' Object with 'microeco' Package

Transform metagenomic classification results of 'mpa' format to 'microtable' object.

Description

Transform the classification results of mpa (MetaPhlAn) format to microtable object, such as MetaPhlAn and Kraken2 results. Kraken2 results can be obtained by merge_metaphlan_tables.py from MetaPhlAn or combine_mpa.py from KrakenTools (https://ccb.jhu.edu/software/krakentools/). The algorithm of Kraken2 determines that the abundance of a taxon is not equal to the sum of abundances of taxa in its subordinate lineage. So the default tables in taxa_abund of return microtable object are extracted from the abundances of raw file. It is totally different with the return taxa_abund of cal_abund function, which sums the abundances of taxa at different taxonomic levels based on the taxonomic table and the otu_table (i.e., taxa abundance table at a specified level, e.g., 's__').

Usage

mpa2meco(
  feature_table,
  sample_table = NULL,
  match_table = NULL,
  use_level = "s__",
  ...
)

Arguments

feature_table	'mpa' format abundance table, see the example.
sample_table	default NULL; sample metadata table; If provided, must be one of the several types of formats: 1) comma seperated file with the suffix csv or tab seperated file with suffix tsv/txt; 2) Excel type file with the suffix xlsx or xls; require readxl package to be installed; 3) data.frame object from R.
match_table	default NULL; a two column table used to replace the sample names in abundance table; Must be two columns without column names; The first column must be raw sample names same with those in feature table, the second column must be new sample names same with the rownames in sample_table; Please also see the example files.
use_level	default "s__"; the prefix parsed for the otu_table and tax_table; must be one of 'd__', 'k__', 'p__', 'c__', 'o__', 'f__', 'g__' and 's__'.
...	parameter passed to microtable$new function of microeco package, such as auto_tidy parameter.

Value

microtable object.

Examples

library(microeco)
library(file2meco)
library(magrittr)
# use Kraken2 file stored inside the package
abund_file_path <- system.file("extdata", "example_kraken2_merge.txt", package="file2meco")
mpa2meco(abund_file_path)
# add sample information table
sample_file_path <- system.file("extdata", "example_metagenome_sample_info.tsv", 
  package="file2meco")
# sample names are different between abund_file_path and sample_file_path; 
# use a matching table to adjust them
match_file_path <- system.file("extdata", "example_metagenome_match_table.tsv", package="file2meco")
test <- mpa2meco(abund_file_path, sample_table = sample_file_path, 
  match_table = match_file_path, use_level = "s__")
# make the taxonomy standard for the following analysis
test$tax_table %<>% tidy_taxonomy
test$tidy_dataset()
# convert the data of default taxa_abund to relative abundance
test$taxa_abund %<>% lapply(function(x){apply(x, 2, function(y){y/sum(y)})})
# calculate taxa_abund with specified level instead of raw kraken results
test1 <- clone(test)
test1$cal_abund()
identical(test$taxa_abund$Kingdom, test1$taxa_abund$Kingdom)

file2meco documentation built on Nov. 10, 2023, 9:09 a.m.