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Filter taxa based on across-sample OTU abundance criteria

Source: R/filter_taxa.R
step_filter_taxa.Rd

This function is directly analogous to the genefilter function for microarray filtering, but is used for filtering OTUs from phyloseq objects. It applies an arbitrary set of functions — as a function list, for instance, created by filterfun — as across-sample criteria, one OTU at a time. It takes as input a phyloseq object, and returns a logical vector indicating whether or not each OTU passed the criteria. Alternatively, if the "prune" option is set to FALSE, it returns the already-trimmed version of the phyloseq object.

Usage

step_filter_taxa(rec, .f, id = rand_id("filter_taxa"))

# S4 method for class 'Recipe'
step_filter_taxa(rec, .f, id = rand_id("filter_taxa"))

Arguments

rec

A Recipe object. The step will be added to the sequence of operations for this Recipe.

.f

A function or list of functions that take a vector of abundance values and return a logical. Some canned useful function types are included in the genefilter-package.

id

A character string that is unique to this step to identify it.

Value

An object of class Recipe

See also

Other filter phy steps: step_filter_by_abundance(), step_filter_by_prevalence(), step_filter_by_rarity(), step_filter_by_variance()

Examples

data(metaHIV_phy)

## Init Recipe
rec <- recipe(metaHIV_phy, "RiskGroup2", "Phylum")
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 Phylum 
#> 
#> 

## Define filter taxa step with default parameters
rec <- 
  step_filter_taxa(rec, .f = "function(x) sum(x > 0) >= (0.03 * length(x))")
  
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 Phylum 
#> 
#> Preporcessing steps:
#> 
#>      ◉ step_filter_taxa() id = filter_taxa__Beaver_Tail 
#> 
#> DA steps:
#>