dar

Introduction

Differential abundance testing in microbiome data challenges both parametric and non-parametric statistical methods, due to its sparsity, high variability and compositional nature. Microbiome-specific statistical methods often assume classical distribution models or take into account compositional specifics. These produce results that range within the specificity vs sensitivity space in such a way that type I and type II error are difficult to ascertain in real microbiome data when a single method is used. Recently, a consensus approach based on multiple differential abundance (DA) methods was recently suggested in order to increase robustness.

With dar, you can use dplyr-like pipeable sequences of DA methods and then apply different consensus strategies. In this way we can obtain more reliable results in a fast, consistent and reproducible way.

Installation

You can install the development version of dar from GitHub with:

# install.packages("devtools")
devtools::install_github("MicrobialGenomics-IrsicaixaOrg/dar")

Usage

library(dar)
#> Registered S3 methods overwritten by 'vegan':
#>   method         from      
#>   reorder.hclust seriation 
#>   rev.hclust     dendextend
data("metaHIV_phy")

## Define recipe
rec <-
  recipe(metaHIV_phy, var_info = "RiskGroup2", tax_info = "Species") %>%
  step_subset_taxa(expr = 'Kingdom %in% c("Bacteria", "Archaea")') %>%
  step_filter_taxa(.f = "function(x) sum(x > 0) >= (0.03 * length(x))") %>%
  step_metagenomeseq(rm_zeros = 0.01) %>%
  step_maaslin()

rec
#> ── DAR Recipe ──────────────────────────────────────────────────────────────────
#> Inputs:
#> 
#>      ℹ phyloseq object with 451 taxa and 156 samples 
#>      ℹ variable of interes RiskGroup2 (class: character, levels: hts, msm, pwid) 
#>      ℹ taxonomic level Species 
#> 
#> Preporcessing steps:
#> 
#>      ◉ step_subset_taxa() id = subset_taxa__Suncake 
#>      ◉ step_filter_taxa() id = filter_taxa__Hot_water_crust_pastry 
#> 
#> DA steps:
#> 
#>      ◉ step_metagenomeseq() id = metagenomeseq__Crocetta_of_Caltanissetta 
#>      ◉ step_maaslin() id = maaslin__Tortita_negra

## Prep recipe
da_results <- prep(rec, parallel = TRUE)
da_results
#> ── DAR Results ─────────────────────────────────────────────────────────────────
#> Inputs:
#> 
#>      ℹ phyloseq object with 278 taxa and 156 samples 
#>      ℹ variable of interes RiskGroup2 (class: character, levels: hts, msm, pwid) 
#>      ℹ taxonomic level Species 
#> 
#> Results:
#> 
#>      ✔ metagenomeseq__Crocetta_of_Caltanissetta diff_taxa = 236 
#>      ✔ maaslin__Tortita_negra diff_taxa = 146 
#> 
#>      ℹ 124 taxa are present in all tested methods

## Consensus strategy
n_methods <- 2
da_results <- bake(da_results, count_cutoff = n_methods)
da_results
#> ── DAR Results ─────────────────────────────────────────────────────────────────
#> Inputs:
#> 
#>      ℹ phyloseq object with 278 taxa and 156 samples 
#>      ℹ variable of interes RiskGroup2 (class: character, levels: hts, msm, pwid) 
#>      ℹ taxonomic level Species 
#> 
#> Results:
#> 
#>      ✔ metagenomeseq__Crocetta_of_Caltanissetta diff_taxa = 236 
#>      ✔ maaslin__Tortita_negra diff_taxa = 146 
#> 
#>      ℹ 124 taxa are present in all tested methods 
#> 
#> Bakes:
#> 
#>      ◉ 1 -> count_cutoff: 2, weights: NULL, exclude: NULL, id: bake__Kürtőskalács

## Results
cool(da_results)
#> ℹ Bake for count_cutoff = 2
#> # A tibble: 124 × 2
#>    taxa_id taxa                   
#>    <chr>   <chr>                  
#>  1 Otu_63  Bacteroides_plebeius   
#>  2 Otu_216 Clostridium_sp_CAG_632 
#>  3 Otu_441 Brachyspira_sp_CAG_700 
#>  4 Otu_108 Prevotella_sp_CAG_520  
#>  5 Otu_257 Butyrivibrio_sp_CAG_318
#>  6 Otu_104 Prevotella_sp_CAG_1092 
#>  7 Otu_69  Bacteroides_sp_CAG_530 
#>  8 Otu_102 Prevotella_sp_AM42_24  
#>  9 Otu_159 Lactobacillus_ruminis  
#> 10 Otu_117 Alistipes_inops        
#> # ℹ 114 more rows

Contributing

• If you think you have encountered a bug, please submit an issue.

• Either way, learn how to create and share a reprex (a minimal, reproducible example), to clearly communicate about your code.

• Working on your first Pull Request? You can learn how from this free series How to Contribute to an Open Source Project on GitHub

Code of Conduct

Please note that the dar project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.