This is a convenience function around the filter_taxa function. It is designed to speed up filtering complex experimental objects with one function call. In the case of run_filter_by_rarity, the filtering will be based on the rarity of each taxon. The taxa retained in the dataset are those where the sum of their rarity is less than the provided threshold.
Usage
step_filter_by_rarity(rec, threshold = 0.01, id = rand_id("filter_by_rarity"))
# S4 method for class 'Recipe'
step_filter_by_rarity(rec, threshold = 0.01, id = rand_id("filter_by_rarity"))
# S4 method for class 'PrepRecipe'
step_filter_by_rarity(rec, threshold = 0.01, id = rand_id("filter_by_rarity"))Arguments
- rec
A Recipe object. The step will be added to the sequence of operations for this Recipe.
- threshold
The rarity threshold for filtering taxa, expressed as a proportion of the total number of samples. For example, a threshold of 0.01 means that a taxon must be present in less than 1% of the samples to be retained. The default value is 0.01.
- id
A character string that is unique to this step to identify it.
Details
The function calculates the rarity of all taxa in the phyloseq object as the proportion of samples in which they are present. It then compares this rarity to the threshold. If a taxon's rarity is greater than the threshold, that taxon is removed from the phyloseq object.
Note
This function modifies rec in place, you might want to make a copy of
rec before modifying it if you need to preserve the original object.
See also
Other filter phy steps:
step_filter_by_abundance(),
step_filter_by_prevalence(),
step_filter_by_variance(),
step_filter_taxa()
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 step_filter_by_rarity step with default parameters
rec <- step_filter_by_rarity(rec, threshold = 0.01)
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_by_rarity() id = filter_by_rarity__Gibanica
#>
#> DA steps:
#>