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Ranked abundance

Source: R/reexports-microbiomeComputations.R
rankedAbundance-methods.Rd

This function returns abundances, ranked by a selected ranking function

Usage

rankedAbundance(
  data,
  method = c("median", "max", "q3", "variance"),
  cutoff = 10,
  verbose = c(TRUE, FALSE)
)

Arguments

data

AbundanceData object

method

string defining the ranking strategy by which to order the taxa. Accepted values are 'median','max','q3',and 'variance'. Note that taxa that return a value of 0 for a given method will not be included in the results.

cutoff

integer indicating the maximium number of taxa to be kept after ranking.

verbose

boolean indicating if timed logging is desired

Value

ComputeResult object

Examples

rankedAbundOutput <- rankedAbundance(
     getCollection(
  microbiomeData::DiabImmune, 
  "16S (V4) Genus (Relative taxonomic abundance analysis)"), 
     method = "median"
)
#> 
#> 2024-06-26 14:29:06.945311 Received df table with 3184 samples and 674 taxa.
#> 
#> 2024-06-26 14:29:07.025819 Finished ranking taxa
#> 
#> 2024-06-26 14:29:07.03636 Ranked abundance computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method = median , cutoff = 10 , naToZero =  TRUE , verbose = TRUE